Bio/Symbol/SymbolI.pm

   1 #
   2 # BioPerl module for Bio::Symbol::SymbolI
   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::SymbolI - Interface for a Symbol
  17
  18 =head1 SYNOPSIS
  19
  20     # get a Bio::Symbol::SymbolI object somehow
  21
  22     my ($name,$token) = ($symbol->name, $symbol->token);
  23     my @symbols       = $symbol->symbols;
  24     my $matches       = $symbol->matches;
  25
  26 =head1 DESCRIPTION
  27
  28 Symbol represents a single token in the sequence. Symbol can have
  29 multiple synonyms or matches within the same Alphabet, which
  30 makes possible to represent ambiguity codes and gaps.
  31
  32 Symbols can be also composed from ordered list other symbols. For
  33 example, codons can be represented by single Symbol using a
  34 compound Alphabet made from three DNA Alphabets.
  35
  36 This module was implemented for the purposes of meeting the
  37 BSANE/BioCORBA spec 0.3 only.
  38
  39 =head1 FEEDBACK
  40
  41 =head2 Mailing Lists
  42
  43 User feedback is an integral part of the evolution of this and other
  44 Bioperl modules. Send your comments and suggestions preferably to
  45 the Bioperl mailing list.  Your participation is much appreciated.
  46
  47   bioperl-l@bioperl.org                  - General discussion
  48   http://bioperl.org/wiki/Mailing_lists  - About the mailing lists
  49
  50 =head2 Support
  51
  52 Please direct usage questions or support issues to the mailing list:
  53
  54 I<bioperl-l@bioperl.org>
  55
  56 rather than to the module maintainer directly. Many experienced and
  57 reponsive experts will be able look at the problem and quickly
  58 address it. Please include a thorough description of the problem
  59 with code and data examples if at all possible.
  60
  61 =head2 Reporting Bugs
  62
  63 Report bugs to the Bioperl bug tracking system to help us keep track
  64 of the bugs and their resolution. Bug reports can be submitted via the
  65 web:
  66
  67   https://redmine.open-bio.org/projects/bioperl/
  68
  69 =head1 AUTHOR - Jason Stajich
  70
  71 Email jason@bioperl.org
  72
  73 =head1 APPENDIX
  74
  75 The rest of the documentation details each of the object methods.
  76 Internal methods are usually preceded with a _
  77
  78 =cut
  79
  80
  81 # Let the code begin...
  82
  83
  84 package Bio::Symbol::SymbolI;
  85 use strict;
  86 use base qw(Bio::Root::RootI);
  87
  88 =head2 Bio::Symbol::SymbolI interface methods
  89
  90 =cut
  91
  92 =head2 name
  93
  94  Title   : name
  95  Usage   : my $name = $symbol->name();
  96  Function: Get/Set Descriptive name for Symbol
  97  Returns : string
  98  Args    : (optional) string
  99
 100 =cut
 101
 102 sub name{
 103    my ($self,@args) = @_;
 104    $self->throw_not_implemented();
 105 }
 106
 107 =head2 token
 108
 109  Title   : token
 110  Usage   : my $token = $self->token();
 111  Function: Get/Set token for this symbol
 112  Example : Letter A,C,G,or T for a DNA alphabet Symbol
 113  Returns : string
 114  Args    : (optional) string
 115
 116 =cut
 117
 118 sub token{
 119    my ($self,@args) = @_;
 120    $self->throw_not_implemented();
 121 }
 122
 123 =head2 symbols
 124
 125  Title   : symbols
 126  Usage   : my @symbols = $self->symbols();
 127  Function: Get/Set Symbols this Symbol is composed from
 128  Example : A codon is composed of 3 DNA symbols
 129  Returns : Array of Bio::Symbol::SymbolI objects
 130  Args    : (optional) Array of Bio::Symbol::SymbolI objects
 131
 132
 133 =cut
 134
 135 sub symbols{
 136    my ($self,@args) = @_;
 137    $self->throw_not_implemented();
 138 }
 139
 140 =head2 matches
 141
 142  Title   : matches
 143  Usage   : my $matchalphabet = $symbol->matches();
 144  Function: Get/Set (Sub) alphabet of symbols matched by this symbol
 145            including the symbol itself (i.e. if symbol is DNA
 146            ambiguity code W then the matches contains symbols for W
 147            and T)
 148  Returns : Bio::Symbol::AlphabetI
 149  Args    : (optional) Bio::Symbol::AlphabetI
 150
 151 =cut
 152
 153 sub matches{
 154    my ($self,@args) = @_;
 155    $self->throw_not_implemented();
 156 }
 157
 158 =head2 equals
 159
 160  Title   : equals
 161  Usage   : if( $symbol->equals($symbol2) ) { }
 162  Function: Tests if a symbol is equal to another
 163  Returns : Boolean
 164  Args    : Bio::Symbol::SymbolI
 165
 166 =cut
 167
 168 sub equals{
 169    my ($self,@args) = @_;
 170    $self->throw_not_implemented();
 171 }
 172
 173 1;