Bio::Symbol ProteinAlphabet
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Summary
Bio::Symbol::ProteinAlphabet - A ready made Protein alphabet
Package variables
No package variables defined.
Included modules
Bio::SeqUtils
Bio::Symbol::Symbol
Bio::Tools::IUPAC
Inherit
Bio::Symbol::Alphabet
Synopsis
    use Bio::Symbol::ProteinAlphabet;
my $alpha = Bio::Symbol::ProteinAlphabet->new();
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 $obj = Bio::Symbol::ProteinAlphabet->new();
Function: Builds a new Bio::Symbol::ProteinAlphabet object
Returns : Bio::Symbol::ProteinAlphabet
Args :
Methods code
newdescriptionprevnextTop
sub new {
  my($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 $let ( keys %codes  ) {  
      if( scalar @{$codes{$let}} != 1) { push @left, $let; next; }
      $symbols{$let} = Bio::Symbol::Symbol->new(-name => $aa{$let},
					       -token => $let);      
  }
  foreach my $l ( @left ) {
      my @subsym;
      foreach my $sym ( @{$codes{$l}} ) {
	  push @subsym, $symbols{$sym};
      }
      my $alpha = Bio::Symbol::Alphabet->new(-symbols =>\@ subsym);
      $symbols{$l} = Bio::Symbol::Symbol->new(-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/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 _