lib/Bio/Symbol/ProteinAlphabet.pm

   1 #
   2 # BioPerl module for Bio::Symbol::ProteinAlphabet
   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::ProteinAlphabet - A ready made Protein alphabet
  17
  18 =head1 SYNOPSIS
  19
  20     use Bio::Symbol::ProteinAlphabet;
  21     my $alpha = Bio::Symbol::ProteinAlphabet->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 Protein 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::ProteinAlphabet;
  76 use strict;
  77
  78 use Bio::Symbol::Symbol;
  79 use Bio::Tools::IUPAC;
  80 use Bio::SeqUtils;
  81
  82 use base qw(Bio::Symbol::Alphabet);
  83
  84 =head2 new
  85
  86  Title   : new
  87  Usage   : my $obj = Bio::Symbol::ProteinAlphabet->new();
  88  Function: Builds a new Bio::Symbol::ProteinAlphabet object
  89  Returns : Bio::Symbol::ProteinAlphabet
  90  Args    :
  91
  92
  93 =cut
  94
  95 sub new {
  96   my($class,@args) = @_;
  97   my $self = $class->SUPER::new(@args);
  98   my %aa = Bio::SeqUtils->valid_aa(2);
  99   my %codes = Bio::Tools::IUPAC->iupac_iup();
 100   my %symbols;
 101   my @left;
 102
 103   foreach my $let ( keys %codes  ) {
 104       if( scalar @{$codes{$let}} != 1) { push @left, $let; next; }
 105       $symbols{$let} = Bio::Symbol::Symbol->new(-name => $aa{$let},
 106                                                -token => $let);
 107   }
 108   foreach my $l ( @left ) {
 109       my @subsym;
 110       foreach my $sym ( @{$codes{$l}} ) {
 111           push @subsym, $symbols{$sym};
 112       }
 113       my $alpha = Bio::Symbol::Alphabet->new(-symbols => \@subsym);
 114       $symbols{$l} = Bio::Symbol::Symbol->new(-name => $aa{$l},
 115                                                -token => $l,
 116                                                -matches => $alpha,
 117                                                -symbols => \@subsym);
 118   }
 119
 120   $self->symbols(values %symbols);
 121   return $self;
 122 }
 123
 124
 125 1;