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1 # $Id: ProteinAlphabet.pm,v 1.3 2002/10/22 07:45:21 lapp Exp $
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2 #
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3 # BioPerl module for Bio::Symbol::ProteinAlphabet
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4 #
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5 # Cared for by Jason Stajich <jason@bioperl.org>
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6 #
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7 # Copyright Jason Stajich
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8 #
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9 # You may distribute this module under the same terms as perl itself
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10
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11 # POD documentation - main docs before the code
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12
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13 =head1 NAME
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14
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15 Bio::Symbol::ProteinAlphabet - A ready made Protein alphabet
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16
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17 =head1 SYNOPSIS
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18
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19 use Bio::Symbol::ProteinAlphabet;
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20 my $alpha = new Bio::Symbol::ProteinAlphabet();
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21 foreach my $symbol ( $alpha->symbols ) {
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22 print "symbol is $symbol\n";
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23 }
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24
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25 =head1 DESCRIPTION
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26
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27 This object builds an Alphabet with Protein symbols.
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28
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29 =head1 FEEDBACK
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30
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31 =head2 Mailing Lists
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32
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33 User feedback is an integral part of the evolution of this and other
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34 Bioperl modules. Send your comments and suggestions preferably to
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35 the Bioperl mailing list. Your participation is much appreciated.
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36
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37 bioperl-l@bioperl.org - General discussion
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38 http://bioperl.org/MailList.shtml - About the mailing lists
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39
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40 =head2 Reporting Bugs
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41
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42 Report bugs to the Bioperl bug tracking system to help us keep track
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43 of the bugs and their resolution. Bug reports can be submitted via
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44 email or the web:
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45
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46 bioperl-bugs@bioperl.org
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47 http://bugzilla.bioperl.org/
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48
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49 =head1 AUTHOR - Jason Stajich
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50
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51 Email jason@bioperl.org
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52
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53 Describe contact details here
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54
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55 =head1 CONTRIBUTORS
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56
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57 Additional contributors names and emails here
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58
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59 =head1 APPENDIX
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60
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61 The rest of the documentation details each of the object methods.
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62 Internal methods are usually preceded with a _
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63
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64 =cut
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65
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66
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67 # Let the code begin...
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68
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69
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70 package Bio::Symbol::ProteinAlphabet;
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71 use vars qw(@ISA);
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72 use strict;
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73
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74 use Bio::Symbol::Alphabet;
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75 use Bio::Symbol::Symbol;
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76 use Bio::Tools::IUPAC;
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77 use Bio::SeqUtils;
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78
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79 @ISA = qw(Bio::Symbol::Alphabet);
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80
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81 =head2 new
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82
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83 Title : new
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84 Usage : my $obj = new Bio::Symbol::ProteinAlphabet();
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85 Function: Builds a new Bio::Symbol::ProteinAlphabet object
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86 Returns : Bio::Symbol::ProteinAlphabet
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87 Args :
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88
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89
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90 =cut
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91
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92 sub new {
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93 my($class,@args) = @_;
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94 my $self = $class->SUPER::new(@args);
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95 my %aa = Bio::SeqUtils->valid_aa(2);
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96 my %codes = Bio::Tools::IUPAC->iupac_iup();
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97 my %symbols;
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98 my @left;
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99
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100 foreach my $let ( keys %codes ) {
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101 next if( $let eq 'U');
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102 if( scalar @{$codes{$let}} != 1) { push @left, $let; next; }
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103 $symbols{$let} = new Bio::Symbol::Symbol(-name => $aa{$let},
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104 -token => $let);
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105 }
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106 foreach my $l ( @left ) {
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107 my @subsym;
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108 foreach my $sym ( @{$codes{$l}} ) {
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109 push @subsym, $symbols{$sym};
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110 }
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111 my $alpha = new Bio::Symbol::Alphabet(-symbols => \@subsym);
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112 $symbols{$l} = new Bio::Symbol::Symbol(-name => $aa{$l},
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113 -token => $l,
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114 -matches => $alpha,
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115 -symbols => \@subsym);
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116 }
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117
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118 $self->symbols(values %symbols);
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119 return $self;
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120 }
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121
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122
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123 1;
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