Bio/Symbol/DNAAlphabet.pm

   1 #
   2 # BioPerl module for Bio::Symbol::DNAAlphabet
   3 #
   4 # Please direct questions and support issues to <bioperl-l@bioperl.org>
   5 #
   6 # Cared for by Jason Stajich <jason@bioperl.org>
   7 #
   8 # Copyright Jason Stajich
   9 #
  10 # You may distribute this module under the same terms as perl itself
  11
  12 # POD documentation - main docs before the code
  13
  14 =head1 NAME
  15
  16 Bio::Symbol::DNAAlphabet - A ready made DNA alphabet
  17
  18 =head1 SYNOPSIS
  19
  20     use Bio::Symbol::DNAAlphabet;
  21     my $alpha = Bio::Symbol::DNAAlphabet->new();
  22     foreach my $symbol ( $alpha->symbols ) {
  23         print "symbol is $symbol\n";
  24     }
  25
  26 =head1 DESCRIPTION
  27
  28 This object builds an Alphabet with DNA symbols.
  29
  30 =head1 FEEDBACK
  31
  32 =head2 Mailing Lists
  33
  34 User feedback is an integral part of the evolution of this and other
  35 Bioperl modules. Send your comments and suggestions preferably to
  36 the Bioperl mailing list.  Your participation is much appreciated.
  37
  38   bioperl-l@bioperl.org                  - General discussion
  39   http://bioperl.org/wiki/Mailing_lists  - About the mailing lists
  40
  41 =head2 Support
  42
  43 Please direct usage questions or support issues to the mailing list:
  44
  45 I<bioperl-l@bioperl.org>
  46
  47 rather than to the module maintainer directly. Many experienced and
  48 reponsive experts will be able look at the problem and quickly
  49 address it. Please include a thorough description of the problem
  50 with code and data examples if at all possible.
  51
  52 =head2 Reporting Bugs
  53
  54 Report bugs to the Bioperl bug tracking system to help us keep track
  55 of the bugs and their resolution. Bug reports can be submitted via the
  56 web:
  57
  58   https://github.com/bioperl/bioperl-live/issues
  59
  60 =head1 AUTHOR - Jason Stajich
  61
  62 Email jason@bioperl.org
  63
  64 =head1 APPENDIX
  65
  66 The rest of the documentation details each of the object methods.
  67 Internal methods are usually preceded with a _
  68
  69 =cut
  70
  71
  72 # Let the code begin...
  73
  74
  75 package Bio::Symbol::DNAAlphabet;
  76 use strict;
  77
  78 use Bio::Symbol::Symbol;
  79 use Bio::Tools::IUPAC;
  80
  81 use base qw(Bio::Symbol::Alphabet);
  82
  83 =head2 new
  84
  85  Title   : new
  86  Usage   : my $obj = Bio::Symbol::DNAAlphabet->new();
  87  Function: Builds a new Bio::Symbol::DNAAlphabet object
  88  Returns : Bio::Symbol::DNAAlphabet
  89  Args    :
  90
  91
  92 =cut
  93
  94 sub new {
  95   my($class,@args) = @_;
  96   my $self = $class->SUPER::new(@args);
  97   my %alphabet = Bio::Tools::IUPAC::iupac_iub();
  98   my %symbols;
  99   foreach my $let ( keys %alphabet ) {
 100       next unless @{$alphabet{$let}} == 1 || $let eq 'U';
 101       $symbols{$let} = Bio::Symbol::Symbol->new(-name => $let,
 102                                                -token => $let);
 103   }
 104
 105   foreach my $let ( keys %alphabet ) {
 106       next if( $symbols{$let} || $let eq 'U');
 107       my @subsymbols;
 108
 109       foreach my $sublet ( @{$alphabet{$let}} ) {
 110           push @subsymbols, $symbols{$sublet};
 111       }
 112       my $alpha = Bio::Symbol::Alphabet->new(-symbols => \@subsymbols);
 113       $symbols{$let} = Bio::Symbol::Symbol->new(-name    => $let,
 114                                                -token   => $let,
 115                                                -matches => $alpha,
 116                                                -symbols => \@subsymbols);
 117   }
 118
 119   $self->symbols(values %symbols);
 120   return $self;
 121 }
 122
 123
 124 1;