Bio::Symbol Symbol
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Summary
Bio::Symbol::Symbol - A biological symbol
Package variables
No package variables defined.
Included modules
Bio::Symbol::Alphabet
Inherit
Bio::Root::Root Bio::Symbol::SymbolI
Synopsis
    use Bio::Symbol::Symbol;
my $thymine = Bio::Symbol::Symbol->new(-name => 'Thy',
-token=> 'T');
my $a = Bio::Symbol::Symbol->new(-token => 'A' );
my $u = Bio::Symbol::Symbol->new(-token => 'U' );
my $g = Bio::Symbol::Symbol->new(-token => 'G' );
my $M = Bio::Symbol::Symbol->new(-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
newDescriptionCode
nameDescriptionCode
tokenDescriptionCode
symbolsDescriptionCode
matchesDescriptionCode
equalsDescriptionCode
Methods description
newcode    nextTop
 Title   : new
Usage : my $obj = Bio::Symbol::Symbol->new();
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.
namecodeprevnextTop
 Title   : name
Usage : my $name = $symbol->name();
Function: Get/Set Descriptive name for Symbol
Returns : string
Args : (optional) string
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
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
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
equalscodeprevnextTop
 Title   : equals
Usage : if( $symbol->equals($symbol2) ) { }
Function: Tests if a symbol is equal to another
Returns : Boolean
Args : Bio::Symbol::SymbolI
Methods code
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 $self;
}
namedescriptionprevnextTop
sub name {
   my ($self,$value) = @_;
   if( $value ) {
       $self->{'_name'} = $value;
   }
   return $self->{'_name'} || '';
}
tokendescriptionprevnextTop
sub token {
   my ($self,$value) = @_;
   if( $value ) {
       $self->{'_token'} = $value;
   }
   return $self->{'_token'} || '';
}
symbolsdescriptionprevnextTop
sub symbols {
   my ($self,@args) = @_;
   if( @args ) {
       $self->{'_symbols'} = [@args];
   } 
   return @{$self->{'_symbols'}};
}
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 $self->{'_matches'};
}
equalsdescriptionprevnextTop
sub equals {
   my ($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;
}
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/wiki/Mailing_lists - About the mailing lists
Support Top
Please direct usage questions or support issues to the mailing list:
bioperl-l@bioperl.org
rather than to the module maintainer directly. Many experienced and
reponsive experts will be able look at the problem and quickly
address it. Please include a thorough description of the problem
with code and data examples if at all possible.
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 the
web:
  https://redmine.open-bio.org/projects/bioperl/
AUTHOR - Jason StajichTop
Email jason@bioperl.org
APPENDIXTop
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _