Bio::Symbol ProteinAlphabet
SummaryIncluded librariesPackage variablesSynopsisDescriptionGeneral documentationMethods
Toolbar
WebCvsRaw content
Summary
Bio::Symbol::ProteinAlphabet - A ready made Protein alphabet
Package variables
No package variables defined.
Included modules
Bio::SeqUtils
Bio::Symbol::Alphabet
Bio::Symbol::Symbol
Bio::Tools::IUPAC
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
newDescriptionCode
Methods description
newcode    nextTop
 Title   : new
Usage : my $obj = new Bio::Symbol::ProteinAlphabet();
Function: Builds a new Bio::Symbol::ProteinAlphabet object
Returns : Bio::Symbol::ProteinAlphabet
Args :
Methods code
newdescriptionprevnextTop
sub new {
  my($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
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 _