lib/Bio/Symbol/AlphabetI.pm

   1 #
   2 # BioPerl module for Bio::Symbol::AlphabetI
   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::AlphabetI - A Symbol Alphabet
  17
  18 =head1 SYNOPSIS
  19
  20     # get a Bio::Symbol::AlphabetI object somehow
  21     my @symbols = $alphabet->symbols;
  22     my @subalphas = $alphabet->alphabets;
  23     if( $alphabet->contains($symbol) ) {
  24         # do something
  25     }
  26
  27 =head1 DESCRIPTION
  28
  29 Alphabet contains set of symbols, which can be concatenated to form
  30 symbol lists. Sequence string, for example, is stringified
  31 representation of the symbol list (tokens of symbols).
  32
  33 This module was implemented for the purposes of meeting the
  34 BSANE/BioCORBA spec 0.3 only.
  35
  36 =head1 FEEDBACK
  37
  38 =head2 Mailing Lists
  39
  40 User feedback is an integral part of the evolution of this and other
  41 Bioperl modules. Send your comments and suggestions preferably to
  42 the Bioperl mailing list.  Your participation is much appreciated.
  43
  44   bioperl-l@bioperl.org                  - General discussion
  45   http://bioperl.org/wiki/Mailing_lists  - About the mailing lists
  46
  47 =head2 Support
  48
  49 Please direct usage questions or support issues to the mailing list:
  50
  51 I<bioperl-l@bioperl.org>
  52
  53 rather than to the module maintainer directly. Many experienced and
  54 reponsive experts will be able look at the problem and quickly
  55 address it. Please include a thorough description of the problem
  56 with code and data examples if at all possible.
  57
  58 =head2 Reporting Bugs
  59
  60 Report bugs to the Bioperl bug tracking system to help us keep track
  61 of the bugs and their resolution. Bug reports can be submitted via the
  62 web:
  63
  64   https://github.com/bioperl/bioperl-live/issues
  65
  66 =head1 AUTHOR - Jason Stajich
  67
  68 Email jason@bioperl.org
  69
  70 =head1 APPENDIX
  71
  72 The rest of the documentation details each of the object methods.
  73 Internal methods are usually preceded with a _
  74
  75 =cut
  76
  77 # Let the code begin...
  78
  79 package Bio::Symbol::AlphabetI;
  80 use strict;
  81 use Bio::Root::RootI;
  82
  83 =head2 AlphabetI Interface methods
  84
  85 =cut
  86
  87 =head2 symbols
  88
  89  Title   : symbols
  90  Usage   : my @symbols = $alphabet->symbols();
  91  Function: Get/Set Symbol list for an alphabet
  92            List of symbols, which make up this alphabet.
  93  Returns : Array of L<Bio::Symbol::SymbolI> objects
  94  Args    : (optional) Array of L<Bio::Symbol::SymbolI> objects
  95
  96 =cut
  97
  98 sub symbols{
  99    my ($self,@args) = @_;
 100    $self->throw_not_implemented();
 101 }
 102
 103 =head2 alphabets
 104
 105  Title   : alphabets
 106  Usage   : my @alphabets = $alphabet->alphabets();
 107  Function: Get/Set Sub Alphabet list for an alphabet
 108            Sub-alphabets. E.g. codons made from DNAxDNAxDNA alphabets
 109  Returns : Array of L<Bio::Symbol::AlphabetI> objects
 110  Args    : (optional) Array of L<Bio::Symbol::AlphabetI> objects
 111
 112 =cut
 113
 114 sub alphabets{
 115     my ($self,@args) = @_;
 116     $self->throw_not_implemented();
 117 }
 118
 119 =head2 contains
 120
 121  Title   : contains
 122  Usage   : if($alphabet->contains($symbol)) { }
 123  Function: Tests of Symbol is contained in this alphabet
 124  Returns : Boolean
 125  Args    : L<Bio::Symbol::SymbolI>
 126
 127 =cut
 128
 129 sub contains{
 130    my ($self,@args) = @_;
 131    $self->throw_not_implemented();
 132 }
 133
 134 # Other methods from BSANE - not sure if we will implement here or only in
 135 # BioCORBA implementation
 136
 137 # Resolve symbols from the token string.
 138 #    SymbolList to_symbol(in string tokens) raises ( IllegalSymbolException) ;
 139
 140 # Convinience method, which returns gap symbol that do not
 141 # match with any other symbols in the alphabet.
 142 #   Symbol get_gap_symbol() raises ( DoesNotExist) ;
 143
 144
 145 # Returns a ambiguity symbol, which represent list of
 146 # symbols. All symbols in a list must be members of
 147 # this alphabet otherwise IllegalSymbolException is
 148 # thrown.
 149 # Symbol get_ambiguity( in SymbolList symbols) raises( IllegalSymbolException);
 150
 151
 152 #  Returns a Symbol, which represents ordered list of symbols
 153 #  given as a parameter. Each symbol in the list must be member of
 154 #  different sub-alphabet in the order defined by the alphabets
 155 #  attribute. For example, codons can be represented by a compound
 156 #  Alphabet of three DNA Alphabets, in which case the get_symbol(
 157 #  SymbolList[ a,g,t]) method of the Alphabet returns Symbol for
 158 #  the codon agt.<p>
 159
 160 #  IllegalSymbolException is raised if members of symbols
 161 #  are not Symbols over the alphabet defined by
 162 #  get_alphabets()-method
 163 #  Symbol get_symbol(in SymbolList symbols) raises(IllegalSymbolException) ;
 164
 165 1;