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1 # $Id: SymbolI.pm,v 1.6 2002/10/22 07:45:21 lapp Exp $
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2 #
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3 # BioPerl module for Bio::Symbol::SymbolI
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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::SymbolI - Interface for a Symbol
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16
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17 =head1 SYNOPSIS
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18
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19 # get a Bio::Symbol::SymbolI object somehow
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20
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21 my ($name,$token) = ($symbol->name, $symbol->token);
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22 my @symbols = $symbol->symbols;
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23 my $matches = $symbol->matches;
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24
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25 =head1 DESCRIPTION
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26
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27 Symbol represents a single token in the sequence. Symbol can have
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28 multiple synonyms or matches within the same Alphabet, which
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29 makes possible to represent ambiguity codes and gaps.
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30
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31 Symbols can be also composed from ordered list other symbols. For
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32 example, codons can be represented by single Symbol using a
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33 compound Alphabet made from three DNA Alphabets.
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34
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35 This module was implemented for the purposes of meeting the
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36 BSANE/BioCORBA spec 0.3 only.
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37
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38 =head1 FEEDBACK
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39
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40 =head2 Mailing Lists
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41
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42 User feedback is an integral part of the evolution of this and other
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43 Bioperl modules. Send your comments and suggestions preferably to
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44 the Bioperl mailing list. Your participation is much appreciated.
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45
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46 bioperl-l@bioperl.org - General discussion
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47 http://bioperl.org/MailList.shtml - About the mailing lists
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48
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49 =head2 Reporting Bugs
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50
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51 Report bugs to the Bioperl bug tracking system to help us keep track
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52 of the bugs and their resolution. Bug reports can be submitted via
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53 email or the web:
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54
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55 bioperl-bugs@bioperl.org
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56 http://bugzilla.bioperl.org/
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57
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58 =head1 AUTHOR - Jason Stajich
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59
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60 Email jason@bioperl.org
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61
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62 =head1 CONTRIBUTORS
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63
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64 Additional contributors names and emails here
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65
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66 =head1 APPENDIX
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67
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68 The rest of the documentation details each of the object methods.
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69 Internal methods are usually preceded with a _
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70
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71 =cut
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72
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73
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74 # Let the code begin...
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75
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76
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77 package Bio::Symbol::SymbolI;
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78 use strict;
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79 use Bio::Root::RootI;
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80 use vars qw(@ISA);
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81 @ISA = qw(Bio::Root::RootI);
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82
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83 =head2 Bio::Symbol::SymbolI interface methods
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84
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85 =cut
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86
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87 =head2 name
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88
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89 Title : name
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90 Usage : my $name = $symbol->name();
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91 Function: Get/Set Descriptive name for Symbol
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92 Returns : string
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93 Args : (optional) string
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94
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95 =cut
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96
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97 sub name{
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98 my ($self,@args) = @_;
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99 $self->throw_not_implemented();
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100 }
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101
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102 =head2 token
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103
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104 Title : token
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105 Usage : my $token = $self->token();
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106 Function: Get/Set token for this symbol
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107 Example : Letter A,C,G,or T for a DNA alphabet Symbol
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108 Returns : string
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109 Args : (optional) string
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110
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111 =cut
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112
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113 sub token{
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114 my ($self,@args) = @_;
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115 $self->throw_not_implemented();
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116 }
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117
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118 =head2 symbols
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119
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120 Title : symbols
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121 Usage : my @symbols = $self->symbols();
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122 Function: Get/Set Symbols this Symbol is composed from
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123 Example : A codon is composed of 3 DNA symbols
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124 Returns : Array of Bio::Symbol::SymbolI objects
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125 Args : (optional) Array of Bio::Symbol::SymbolI objects
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126
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127
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128 =cut
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129
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130 sub symbols{
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131 my ($self,@args) = @_;
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132 $self->throw_not_implemented();
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133 }
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134
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135 =head2 matches
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136
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137 Title : matches
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138 Usage : my $matchalphabet = $symbol->matches();
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139 Function: Get/Set (Sub) alphabet of symbols matched by this symbol
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140 including the symbol itself (i.e. if symbol is DNA
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141 ambiguity code W then the matches contains symbols for W
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142 and T)
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143 Returns : Bio::Symbol::AlphabetI
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144 Args : (optional) Bio::Symbol::AlphabetI
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145
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146 =cut
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147
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148 sub matches{
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149 my ($self,@args) = @_;
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150 $self->throw_not_implemented();
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151 }
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152
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153 =head2 equals
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154
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155 Title : equals
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156 Usage : if( $symbol->equals($symbol2) ) { }
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157 Function: Tests if a symbol is equal to another
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158 Returns : Boolean
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159 Args : Bio::Symbol::SymbolI
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160
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161 =cut
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162
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163 sub equals{
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164 my ($self,@args) = @_;
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165 $self->throw_not_implemented();
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166 }
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167
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168 1;
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