Bio/Symbol/ProteinAlphabet.pm

   1 # $Id$
   2 #
   3 # BioPerl module for Bio::Symbol::ProteinAlphabet
   4 #
   5 # Please direct questions and support issues to <bioperl-l@bioperl.org>
   6 #
   7 # Cared for by Jason Stajich <jason@bioperl.org>
   8 #
   9 # Copyright Jason Stajich
  10 #
  11 # You may distribute this module under the same terms as perl itself
  12
  13 # POD documentation - main docs before the code
  14
  15 =head1 NAME
  16
  17 Bio::Symbol::ProteinAlphabet - A ready made Protein alphabet
  18
  19 =head1 SYNOPSIS
  20
  21     use Bio::Symbol::ProteinAlphabet;
  22     my $alpha = Bio::Symbol::ProteinAlphabet->new();
  23     foreach my $symbol ( $alpha->symbols ) {
  24         print "symbol is $symbol\n";
  25     }
  26
  27 =head1 DESCRIPTION
  28
  29 This object builds an Alphabet with Protein symbols.
  30
  31 =head1 FEEDBACK
  32
  33 =head2 Mailing Lists
  34
  35 User feedback is an integral part of the evolution of this and other
  36 Bioperl modules. Send your comments and suggestions preferably to
  37 the Bioperl mailing list.  Your participation is much appreciated.
  38
  39   bioperl-l@bioperl.org                  - General discussion
  40   http://bioperl.org/wiki/Mailing_lists  - About the mailing lists
  41
  42 =head2 Support
  43
  44 Please direct usage questions or support issues to the mailing list:
  45
  46 L<bioperl-l@bioperl.org>
  47
  48 rather than to the module maintainer directly. Many experienced and
  49 reponsive experts will be able look at the problem and quickly
  50 address it. Please include a thorough description of the problem
  51 with code and data examples if at all possible.
  52
  53 =head2 Reporting Bugs
  54
  55 Report bugs to the Bioperl bug tracking system to help us keep track
  56 of the bugs and their resolution. Bug reports can be submitted via the
  57 web:
  58
  59   http://bugzilla.open-bio.org/
  60
  61 =head1 AUTHOR - Jason Stajich
  62
  63 Email jason@bioperl.org
  64
  65 =head1 APPENDIX
  66
  67 The rest of the documentation details each of the object methods.
  68 Internal methods are usually preceded with a _
  69
  70 =cut
  71
  72
  73 # Let the code begin...
  74
  75
  76 package Bio::Symbol::ProteinAlphabet;
  77 use strict;
  78
  79 use Bio::Symbol::Symbol;
  80 use Bio::Tools::IUPAC;
  81 use Bio::SeqUtils;
  82
  83 use base qw(Bio::Symbol::Alphabet);
  84
  85 =head2 new
  86
  87  Title   : new
  88  Usage   : my $obj = Bio::Symbol::ProteinAlphabet->new();
  89  Function: Builds a new Bio::Symbol::ProteinAlphabet object
  90  Returns : Bio::Symbol::ProteinAlphabet
  91  Args    :
  92
  93
  94 =cut
  95
  96 sub new {
  97   my($class,@args) = @_;
  98   my $self = $class->SUPER::new(@args);
  99   my %aa = Bio::SeqUtils->valid_aa(2);
 100   my %codes = Bio::Tools::IUPAC->iupac_iup();
 101   my %symbols;
 102   my @left;
 103
 104   foreach my $let ( keys %codes  ) {
 105       if( scalar @{$codes{$let}} != 1) { push @left, $let; next; }
 106       $symbols{$let} = Bio::Symbol::Symbol->new(-name => $aa{$let},
 107                                                -token => $let);
 108   }
 109   foreach my $l ( @left ) {
 110       my @subsym;
 111       foreach my $sym ( @{$codes{$l}} ) {
 112           push @subsym, $symbols{$sym};
 113       }
 114       my $alpha = Bio::Symbol::Alphabet->new(-symbols => \@subsym);
 115       $symbols{$l} = Bio::Symbol::Symbol->new(-name => $aa{$l},
 116                                                -token => $l,
 117                                                -matches => $alpha,
 118                                                -symbols => \@subsym);
 119   }
 120
 121   $self->symbols(values %symbols);
 122   return $self;
 123 }
 124
 125
 126 1;