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1 # $Id: AlphabetI.pm,v 1.5 2002/10/22 07:45:21 lapp Exp $
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2 #
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3 # BioPerl module for Bio::Symbol::AlphabetI
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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::AlphabetI - A Symbol Alphabet
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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::AlphabetI object somehow
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20 my @symbols = $alphabet->symbols;
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21 my @subalphas = $alphabet->alphabets;
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22 if( $alphabet->contains($symbol) ) {
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23 # do something
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24 }
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25
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26 =head1 DESCRIPTION
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27
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28 Alphabet contains set of symbols, which can be concatenated to form
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29 symbol lists. Sequence string, for example, is stringified
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30 representation of the symbol list (tokens of symbols).
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31
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32 This module was implemented for the purposes of meeting the
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33 BSANE/BioCORBA spec 0.3 only.
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34
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35 =head1 FEEDBACK
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36
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37 =head2 Mailing Lists
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38
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39 User feedback is an integral part of the evolution of this and other
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40 Bioperl modules. Send your comments and suggestions preferably to
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41 the Bioperl mailing list. Your participation is much appreciated.
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42
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43 bioperl-l@bioperl.org - General discussion
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44 http://bioperl.org/MailList.shtml - About the mailing lists
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45
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46 =head2 Reporting Bugs
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47
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48 Report bugs to the Bioperl bug tracking system to help us keep track
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49 of the bugs and their resolution. Bug reports can be submitted via
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50 email or the web:
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51
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52 bioperl-bugs@bioperl.org
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53 http://bugzilla.bioperl.org/
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54
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55 =head1 AUTHOR - Jason Stajich
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56
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57 Email jason@bioperl.org
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58
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59 Describe contact details here
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60
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61 =head1 CONTRIBUTORS
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62
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63 Additional contributors names and emails here
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64
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65 =head1 APPENDIX
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66
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67 The rest of the documentation details each of the object methods.
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68 Internal methods are usually preceded with a _
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69
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70 =cut
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71
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72 # Let the code begin...
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73
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74 package Bio::Symbol::AlphabetI;
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75 use strict;
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76 use Bio::Root::RootI;
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77
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78 =head2 AlphabetI Interface methods
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79
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80 =cut
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81
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82 =head2 symbols
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83
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84 Title : symbols
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85 Usage : my @symbols = $alphabet->symbols();
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86 Function: Get/Set Symbol list for an alphabet
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87 List of symbols, which make up this alphabet.
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88 Returns : Array of L<Bio::Symbol::SymbolI> objects
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89 Args : (optional) Array of L<Bio::Symbol::SymbolI> objects
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90
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91 =cut
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92
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93 sub symbols{
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94 my ($self,@args) = @_;
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95 $self->throw_not_implemented();
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96 }
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97
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98 =head2 alphabets
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99
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100 Title : alphabets
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101 Usage : my @alphabets = $alphabet->alphabets();
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102 Function: Get/Set Sub Alphabet list for an alphabet
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103 Sub-alphabets. E.g. codons made from DNAxDNAxDNA alphabets
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104 Returns : Array of L<Bio::Symbol::AlphabetI> objects
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105 Args : (optional) Array of L<Bio::Symbol::AlphabetI> objects
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106
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107 =cut
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108
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109 sub alphabets{
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110 my ($self,@args) = @_;
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111 $self->throw_not_implemented();
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112 }
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113
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114 =head2 contains
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115
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116 Title : contains
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117 Usage : if($alphabet->contains($symbol)) { }
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118 Function: Tests of Symbol is contained in this alphabet
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119 Returns : Boolean
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120 Args : L<Bio::Symbol::SymbolI>
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121
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122 =cut
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123
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124 sub contains{
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125 my ($self,@args) = @_;
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126 $self->throw_not_implemented();
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127 }
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128
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129 # Other methods from BSANE - not sure if we will implement here or only in
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130 # BioCORBA implementation
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131
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132 # Resolve symbols from the token string.
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133 # SymbolList to_symbol(in string tokens) raises ( IllegalSymbolException) ;
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134
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135 # Convinience method, which returns gap symbol that do not
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136 # match with any other symbols in the alphabet.
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137 # Symbol get_gap_symbol() raises ( DoesNotExist) ;
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138
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139
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140 # Returns a ambiguity symbol, which represent list of
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141 # symbols. All symbols in a list must be members of
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142 # this alphabet otherwise IllegalSymbolException is
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143 # thrown.
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144 # Symbol get_ambiguity( in SymbolList symbols) raises( IllegalSymbolException);
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145
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146
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147 # Returns a Symbol, which represents ordered list of symbols
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148 # given as a parameter. Each symbol in the list must be member of
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149 # different sub-alphabet in the order defined by the alphabets
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150 # attribute. For example, codons can be represented by a compound
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151 # Alphabet of three DNA Alphabets, in which case the get_symbol(
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152 # SymbolList[ a,g,t]) method of the Alphabet returns Symbol for
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153 # the codon agt.<p>
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154
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155 # IllegalSymbolException is raised if members of symbols
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156 # are not Symbols over the alphabet defined by
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157 # get_alphabets()-method
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158 # Symbol get_symbol(in SymbolList symbols) raises(IllegalSymbolException) ;
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159
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160 1;
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