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Summary

Bio::Symbol::DNAAlphabet - A ready made DNA alphabet

Package variables

Included modules

Inherit

Bio::Symbol::Alphabet

Synopsis

    use Bio::Symbol::DNAAlphabet;
    my $alpha = Bio::Symbol::DNAAlphabet->new();
    foreach my $symbol ( $alpha->symbols ) {
	print "symbol is $symbol\n";
    }

Description

This object builds an Alphabet with DNA symbols.

Methods

Methods description

 Title   : new
 Usage   : my $obj = Bio::Symbol::DNAAlphabet->new();
 Function: Builds a new Bio::Symbol::DNAAlphabet object 
 Returns : Bio::Symbol::DNAAlphabet
 Args    :

Methods code

sub new {

  my($class,@args) = @_;
  my $self = $class->SUPER::new(@args);  
  my %alphabet = Bio::Tools::IUPAC::iupac_iub();
  my %symbols;
  foreach my $let ( keys %alphabet ) {
      next unless @{$alphabet{$let}} == 1 || $let eq 'U';
      $symbols{$let} = Bio::Symbol::Symbol->new(-name => $let,
					       -token => $let);      
  }
  
  foreach my $let ( keys %alphabet ) {
      next if( $symbols{$let} || $let eq 'U');
      my @subsymbols;
      
      foreach my $sublet ( @{$alphabet{$let}} ) {
	  push @subsymbols, $symbols{$sublet};
      }
      my $alpha = Bio::Symbol::Alphabet->new(-symbols =>\@ subsymbols);
      $symbols{$let} = Bio::Symbol::Symbol->new(-name    => $let,
					       -token   => $let,
					       -matches => $alpha,  
					       -symbols =>\@ subsymbols); 
  }
  
  $self->symbols(values %symbols); 
  return $self;
}


1;

}

General documentation

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with code and data examples if at all possible.

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