Bio::Symbol Symbol
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Summary
Bio::Symbol::Symbol - A biological symbol
Package variables
No package variables defined.
Included modules
Bio::Root::Root
Bio::Symbol::Alphabet
Bio::Symbol::SymbolI
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
equalsDescriptionCode
matchesDescriptionCode
nameDescriptionCode
newDescriptionCode
symbolsDescriptionCode
tokenDescriptionCode
Methods description
equalscode    nextTop
 Title   : equals
Usage : if( $symbol->equals($symbol2) ) { }
Function: Tests if a symbol is equal to another
Returns : Boolean
Args : Bio::Symbol::SymbolI
matchescodeprevnextTop
 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
namecodeprevnextTop
 Title   : name
Usage : my $name = $symbol->name();
Function: Get/Set Descriptive name for Symbol
Returns : string
Args : (optional) string
newcodeprevnextTop
 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.
symbolscodeprevnextTop
 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
tokencodeprevnextTop
 Title   : token
Usage : my $token = $self->token();
Function: Get/Set token for this symbol
Example : Letter A,C,G,or T for a DNA alphabet Symbol
Returns : string
Args : (optional) string
Methods code
equalsdescriptionprevnextTop
sub equals {
   my ($self,$symbol2) = @_;
   # Let's just test based on Tokens for now 
# Doesn't handle DNA vs PROTEIN accidential comparisons
return $self->token eq $symbol2->token; } 1;
}
matchesdescriptionprevnextTop
sub matches {
   my ($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 $self->{'_matches'};
}
namedescriptionprevnextTop
sub name {
   my ($self,$value) = @_;
   if( $value ) {
       $self->{'_name'} = $value;
   }
   return $self->{'_name'} || '';
}
newdescriptionprevnextTop
sub new {
  my($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 $self;
}
symbolsdescriptionprevnextTop
sub symbols {
   my ($self,@args) = @_;
   if( @args ) {
       $self->{'_symbols'} = [@args];
   } 
   return @{$self->{'_symbols'}};
}
tokendescriptionprevnextTop
sub token {
   my ($self,$value) = @_;
   if( $value ) {
       $self->{'_token'} = $value;
   }
   return $self->{'_token'} || '';
}
General documentation
FEEDBACKTop
Mailing ListsTop
User feedback is an integral part of the evolution of this and other
Bioperl modules. Send your comments and suggestions preferably to
the Bioperl mailing list. Your participation is much appreciated.
  bioperl-l@bioperl.org              - General discussion
http://bioperl.org/MailList.shtml - About the mailing lists
Reporting BugsTop
Report bugs to the Bioperl bug tracking system to help us keep track
of the bugs and their resolution. Bug reports can be submitted via
email or the web:
  bioperl-bugs@bioperl.org
http://bugzilla.bioperl.org/
AUTHOR - Jason StajichTop
Email jason@bioperl.org
Describe contact details here
CONTRIBUTORSTop
Additional contributors names and emails here
APPENDIXTop
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _