Summary

Bio::Symbol::Symbol - A biological symbol

Package variables

Included modules

Inherit

Bio::Root::Root Bio::Symbol::SymbolI

Synopsis

    use Bio::Symbol::Symbol;
    my $thymine = new Bio::Symbol::Symbol(-name => 'Thy',
					  -token=> 'T');
    my $a = new Bio::Symbol::Symbol(-token => 'A' );
    my $u = new Bio::Symbol::Symbol(-token => 'U' );
    my $g = new Bio::Symbol::Symbol(-token => 'G' );

    my $M = new Bio::Symbol::Symbol(-name  => 'Met',
				    -token => 'M',
				    -symbols => [ $a, $u, $g ]);

    my ($name,$token) = ($a->name, $a->token);
    my @symbols       = $a->symbols;
    my $matches       = $a->matches;

Description

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.

Methods

Methods description

 Title   : new
 Usage   : my $obj = new Bio::Symbol::Symbol();
 Function: Builds a new Bio::Symbol::Symbol object 
 Returns : Bio::Symbol::Symbol
 Args    : -name    => descriptive name (string) [e.g. Met]
           -token   => Shorthand token (string)  [e.g. M]
           -symbols => Symbols that make up this symbol (array) [e.g. AUG]
           -matches => Alphabet in the event symbol is an ambiguity
                       code.

 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 : Ambiguity symbols are made up > 1 base symbol
 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

Methods code

sub new {

  my($class,@args) = @_;
  my $self = $class->SUPER::new(@args);
  $self->{'_symbols'} = [];

  my ($name, $token, $symbols,
      $matches) = $self->_rearrange([qw(NAME TOKEN SYMBOLS 
					MATCHES)],
				    @args);
  $token && $self->token($token);
  $name && $self->name($name);
  $symbols && ref($symbols) =~ /array/i && $self->symbols(@$symbols);
  $matches && $self->matches($matches); 
  return $self;

}

sub name {

   my ($self,$value) = @_;
   if( $value ) {
       $self->{'_name'} = $value;
   }
   return $self->{'_name'} || '';

}

sub token {

   my ($self,$value) = @_;
   if( $value ) {
       $self->{'_token'} = $value;
   }
   return $self->{'_token'} || '';

}

sub symbols {

   my ($self,@args) = @_;
   if( @args ) {
       $self->{'_symbols'} = [@args];
   } 
   return @{$self->{'_symbols'}};

}

sub matches {

   my ($self,$matches) = @_;
   
   if( $matches ) {
       if( ! $matches->isa('Bio::Symbol::AlphabetI') ) {
	   $self->warn("Must pass in a Bio::Symbol::AlphabetI object to matches function");
	   # stick with previous value
       } else { 
	   $self->{'_matches'} = $matches;
       }
   }
   return $self->{'_matches'};

}

sub equals {

   my ($self,$symbol2) = @_;
   # Let's just test based on Tokens for now 
   # Doesn't handle DNA vs PROTEIN accidential comparisons
   return  $self->token eq $symbol2->token;

}

General documentation

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