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Summary

Bio::Symbol::Alphabet - DESCRIPTION of Object

Package variables

Included modules

Inherit

Bio::Root::Root Bio::Symbol::AlphabetI

Synopsis

  {
      my $alphabet = new Bio::Symbols::Alphabet(-symbols => [ @s ],
  						-subalphabets => [ @alphas ] );

      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   : new
 Usage   : my $obj = new Bio::Symbol::Alphabet();
 Function: Builds a new Bio::Symbol::Alphabet object 
 Returns : Bio::Symbol::Alphabet
 Args    : -symbols  => Array ref of Bio::Symbol::SymbolI objects
           -subalphas=> Array ref of Bio::Symbol::AlphabetI objects 
                        representing sub alphabets

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

Methods code

sub alphabets {

    my ($self,@args) = @_;
   if( @args ) { 
       $self->{'_alphabets'} = [];
       foreach my $alpha ( @args ) {
	   if( ! $alpha->isa('Bio::Symbol::AlphabetI') ) {
	       $self->warn("Did not provide a proper Bio::Symbol::AlphabetI to method 'alphabets' (got $alpha)");
	   } else { 
	       push @{$self->{'_alphabets'}}, $alpha;
	   }
       }
   }
    return @{$self->{'_alphabets'}};

}

sub contains {

   my ($self,$testsymbol) = @_;
   foreach my $symbol ( $self->symbols ) {
       return 1 if( $symbol->equals($testsymbol) );
   }
   return 0;
}

1;

}

sub new {

    my($class,@args) = @_;

    my $self = $class->SUPER::new(@args);
    $self->{'_symbols'} = [];
    $self->{'_alphabets'} = [];
    my ($symbols, $subalphas) = $self->_rearrange([qw(SYMBOLS SUBALPHAS)],
						  @args);

    defined $symbols && ref($symbols) =~ /array/i && $self->symbols(@$symbols);
    defined $subalphas && ref($subalphas) =~ /array/i && $self->alphabets(@$subalphas);
    return $self;

}

sub symbols {

    my ($self,@args) = @_;
    if( @args ) { 
	$self->{'_symbols'} = [];
	foreach my $symbol ( @args ) {
	    if( ! defined $symbol || ! ref($symbol) || 
		! $symbol->isa('Bio::Symbol::SymbolI') ) {
		$self->warn("Did not provide a proper Bio::Symbol::SymbolI to method 'symbols' (got $symbol)");
	    } else { 
		push @{$self->{'_symbols'}}, $symbol;
	    }
	}
    }
    return @{$self->{'_symbols'}};

}

General documentation

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