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Summary

Bio::Symbol::ProteinAlphabet - A ready made Protein alphabet

Package variables

Included modules

Inherit

Bio::Symbol::Alphabet

Synopsis

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

Description

This object builds an Alphabet with Protein symbols.

Methods

Methods description

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

Methods code

sub new {

  my($class,@args) = @_;
  my $self = $class->SUPER::new(@args);  
  my %aa = Bio::SeqUtils->valid_aa(2);
  my %codes = Bio::Tools::IUPAC->iupac_iup();
  my %symbols;
  my @left;
  
  foreach my $let ( keys %codes  ) {  
      next if( $let eq 'U');
      if( scalar @{$codes{$let}} != 1) { push @left, $let; next; }
      $symbols{$let} = new Bio::Symbol::Symbol(-name => $aa{$let},
					       -token => $let);      
  }
  foreach my $l ( @left ) {
      my @subsym;
      foreach my $sym ( @{$codes{$l}} ) {
	  push @subsym, $symbols{$sym};
      }
      my $alpha = new Bio::Symbol::Alphabet(-symbols =>\@ subsym);
      $symbols{$l} = new Bio::Symbol::Symbol(-name => $aa{$l},
					       -token => $l,
					       -matches => $alpha,
					       -symbols =>\@ subsym);
  }
  
  $self->symbols(values %symbols); 
  return $self;
}


1;

}

General documentation

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The rest of the documentation details each of the object methods.
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