Raw content of Bio::Symbol::DNAAlphabet # $Id: DNAAlphabet.pm,v 1.3 2002/10/22 07:45:21 lapp Exp $ # # BioPerl module for Bio::Symbol::DNAAlphabet # # Cared for by Jason Stajich <jason@bioperl.org> # # Copyright Jason Stajich # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::Symbol::DNAAlphabet - A ready made DNA alphabet =head1 SYNOPSIS use Bio::Symbol::DNAAlphabet; my $alpha = new Bio::Symbol::DNAAlphabet(); foreach my $symbol ( $alpha->symbols ) { print "symbol is $symbol\n"; } =head1 DESCRIPTION This object builds an Alphabet with DNA symbols. =head1 FEEDBACK =head2 Mailing Lists 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 =head2 Reporting Bugs 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/ =head1 AUTHOR - Jason Stajich Email jason@bioperl.org Describe contact details here =head1 CONTRIBUTORS Additional contributors names and emails here =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::Symbol::DNAAlphabet; use vars qw(@ISA); use strict; use Bio::Symbol::Alphabet; use Bio::Symbol::Symbol; use Bio::Tools::IUPAC; @ISA = qw(Bio::Symbol::Alphabet); =head2 new Title : new Usage : my $obj = new Bio::Symbol::DNAAlphabet(); Function: Builds a new Bio::Symbol::DNAAlphabet object Returns : Bio::Symbol::DNAAlphabet Args : =cut sub new { my($class,@args) = @_; my $self = $class->SUPER::new(@args); my %alphabet = Bio::Tools::IUPAC::iupac_iub(); my %symbols; foreach my $let ( keys %alphabet ) { next unless @{$alphabet{$let}} == 1 || $let eq 'U'; $symbols{$let} = new Bio::Symbol::Symbol(-name => $let, -token => $let); } foreach my $let ( keys %alphabet ) { next if( $symbols{$let} || $let eq 'U'); my @subsymbols; foreach my $sublet ( @{$alphabet{$let}} ) { push @subsymbols, $symbols{$sublet}; } my $alpha = new Bio::Symbol::Alphabet(-symbols => \@subsymbols); $symbols{$let} = new Bio::Symbol::Symbol(-name => $let, -token => $let, -matches => $alpha, -symbols => \@subsymbols); } $self->symbols(values %symbols); return $self; } 1;