lib/Bio/Symbol/Alphabet.pm

   1 #
   2 # BioPerl module for Bio::Symbol::Alphabet
   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::Alphabet - BSANE/BioCORBA compliant symbol list alphabet
  17
  18 =head1 SYNOPSIS
  19
  20   {
  21       my $alphabet = Bio::Symbols::Alphabet->new(-symbols => [ @s ],
  22                                                 -subalphabets => [ @alphas ] );
  23
  24       my @symbols = $alphabet->symbols;
  25       my @subalphas = $alphabet->alphabets;
  26       if( $alphabet->contains($symbol) ) {
  27           # do something
  28       }
  29   }
  30
  31 =head1 DESCRIPTION
  32
  33 Alphabet contains set of symbols, which can be concatenated to
  34 form symbol lists. Sequence string, for example, is stringified
  35 representation of the symbol list (tokens of symbols).
  36
  37 This module was implemented for the purposes of meeting the
  38 BSANE/BioCORBA spec 0.3 only.
  39
  40 =head1 FEEDBACK
  41
  42 =head2 Mailing Lists
  43
  44 User feedback is an integral part of the evolution of this and other
  45 Bioperl modules. Send your comments and suggestions preferably to
  46 the Bioperl mailing list.  Your participation is much appreciated.
  47
  48   bioperl-l@bioperl.org                  - General discussion
  49   http://bioperl.org/wiki/Mailing_lists  - About the mailing lists
  50
  51 =head2 Support
  52
  53 Please direct usage questions or support issues to the mailing list:
  54
  55 I<bioperl-l@bioperl.org>
  56
  57 rather than to the module maintainer directly. Many experienced and
  58 reponsive experts will be able look at the problem and quickly
  59 address it. Please include a thorough description of the problem
  60 with code and data examples if at all possible.
  61
  62 =head2 Reporting Bugs
  63
  64 Report bugs to the Bioperl bug tracking system to help us keep track
  65 of the bugs and their resolution. Bug reports can be submitted via the
  66 web:
  67
  68   https://github.com/bioperl/bioperl-live/issues
  69
  70 =head1 AUTHOR - Jason Stajich
  71
  72 Email jason@bioperl.org
  73
  74 =head1 APPENDIX
  75
  76 The rest of the documentation details each of the object methods.
  77 Internal methods are usually preceded with a _
  78
  79 =cut
  80
  81
  82 # Let the code begin...
  83
  84
  85 package Bio::Symbol::Alphabet;
  86 use strict;
  87
  88 # Object preamble - inherits from Bio::Root::Root
  89
  90
  91 use base qw(Bio::Root::Root Bio::Symbol::AlphabetI);
  92
  93 =head2 new
  94
  95  Title   : new
  96  Usage   : my $obj = Bio::Symbol::Alphabet->new();
  97  Function: Builds a new Bio::Symbol::Alphabet object
  98  Returns : Bio::Symbol::Alphabet
  99  Args    : -symbols  => Array ref of Bio::Symbol::SymbolI objects
 100            -subalphas=> Array ref of Bio::Symbol::AlphabetI objects
 101                         representing sub alphabets
 102
 103 =cut
 104
 105 sub new {
 106     my($class,@args) = @_;
 107
 108     my $self = $class->SUPER::new(@args);
 109     $self->{'_symbols'} = [];
 110     $self->{'_alphabets'} = [];
 111     my ($symbols, $subalphas) = $self->_rearrange([qw(SYMBOLS SUBALPHAS)],
 112                                                   @args);
 113
 114     defined $symbols && ref($symbols) =~ /array/i && $self->symbols(@$symbols);
 115     defined $subalphas && ref($subalphas) =~ /array/i && $self->alphabets(@$subalphas);
 116     return $self;
 117 }
 118
 119 =head2 AlphabetI Interface methods
 120
 121 =cut
 122
 123 =head2 symbols
 124
 125  Title   : symbols
 126  Usage   : my @symbols = $alphabet->symbols();
 127  Function: Get/Set Symbol list for an alphabet
 128            List of symbols, which make up this alphabet.
 129  Returns : Array of Bio::Symbol::SymbolI objects
 130  Args    : (optionalalphabets) Array of Bio::Symbol::SymbolI objects
 131
 132 =cut
 133
 134 sub symbols {
 135     my ($self,@args) = @_;
 136     if( @args ) {
 137         $self->{'_symbols'} = [];
 138         foreach my $symbol ( @args ) {
 139             if( ! defined $symbol || ! ref($symbol) ||
 140                 ! $symbol->isa('Bio::Symbol::SymbolI') ) {
 141                 $self->warn("Did not provide a proper Bio::Symbol::SymbolI to method 'symbols' (got $symbol)");
 142             } else {
 143                 push @{$self->{'_symbols'}}, $symbol;
 144             }
 145         }
 146     }
 147     return @{$self->{'_symbols'}};
 148 }
 149
 150 =head2 alphabets
 151
 152  Title   : alphabets
 153  Usage   : my @alphabets = $alphabet->alphabets();
 154  Function: Get/Set Sub Alphabet list for an alphabet
 155            Sub-alphabets. E.g. codons made from DNAxDNAxDNA alphabets
 156  Returns : Array of Bio::Symbol::AlphabetI objects
 157  Args    : (optional) Array of Bio::Symbol::AlphabetI objects
 158
 159 =cut
 160
 161 sub alphabets {
 162     my ($self,@args) = @_;
 163    if( @args ) {
 164        $self->{'_alphabets'} = [];
 165        foreach my $alpha ( @args ) {
 166            if( ! $alpha->isa('Bio::Symbol::AlphabetI') ) {
 167                $self->warn("Did not provide a proper Bio::Symbol::AlphabetI to method 'alphabets' (got $alpha)");
 168            } else {
 169                push @{$self->{'_alphabets'}}, $alpha;
 170            }
 171        }
 172    }
 173     return @{$self->{'_alphabets'}};
 174 }
 175
 176 =head2 contains
 177
 178  Title   : contains
 179  Usage   : if($alphabet->contains($symbol)) { }
 180  Function: Tests of Symbol is contained in this alphabet
 181  Returns : Boolean
 182  Args    : Bio::Symbol::SymbolI
 183
 184 =cut
 185
 186 sub contains{
 187    my ($self,$testsymbol) = @_;
 188    foreach my $symbol ( $self->symbols ) {
 189        return 1 if( $symbol->equals($testsymbol) );
 190    }
 191    return 0;
 192 }
 193
 194 1;