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1 # $Id: Alphabet.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::Alphabet
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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::Alphabet - DESCRIPTION of Object
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16
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17 =head1 SYNOPSIS
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18
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19 {
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20 my $alphabet = new Bio::Symbols::Alphabet(-symbols => [ @s ],
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21 -subalphabets => [ @alphas ] );
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22
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23 my @symbols = $alphabet->symbols;
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24 my @subalphas = $alphabet->alphabets;
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25 if( $alphabet->contains($symbol) ) {
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26 # do something
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27 }
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28 }
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29
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30 =head1 DESCRIPTION
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31
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32 Alphabet contains set of symbols, which can be concatenated to
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33 form symbol lists. Sequence string, for example, is stringified
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34 representation of the symbol list (tokens of symbols).
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35
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36 This module was implemented for the purposes of meeting the
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37 BSANE/BioCORBA spec 0.3 only.
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38
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39 =head1 FEEDBACK
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40
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41 =head2 Mailing Lists
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42
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43 User feedback is an integral part of the evolution of this and other
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44 Bioperl modules. Send your comments and suggestions preferably to
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45 the Bioperl mailing list. Your participation is much appreciated.
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46
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47 bioperl-l@bioperl.org - General discussion
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48 http://bioperl.org/MailList.shtml - About the mailing lists
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49
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50 =head2 Reporting Bugs
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51
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52 Report bugs to the Bioperl bug tracking system to help us keep track
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53 of the bugs and their resolution. Bug reports can be submitted via
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54 email or the web:
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55
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56 bioperl-bugs@bioperl.org
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57 http://bugzilla.bioperl.org/
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58
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59 =head1 AUTHOR - Jason Stajich
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60
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61 Email jason@bioperl.org
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62
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63 Describe contact details here
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64
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65 =head1 CONTRIBUTORS
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66
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67 Additional contributors names and emails here
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68
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69 =head1 APPENDIX
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70
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71 The rest of the documentation details each of the object methods.
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72 Internal methods are usually preceded with a _
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73
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74 =cut
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75
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76
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77 # Let the code begin...
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78
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79
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80 package Bio::Symbol::Alphabet;
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81 use vars qw(@ISA);
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82 use strict;
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83
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84 # Object preamble - inherits from Bio::Root::Root
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85
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86 use Bio::Root::Root;
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87 use Bio::Symbol::AlphabetI;
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88
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89 @ISA = qw(Bio::Root::Root Bio::Symbol::AlphabetI );
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90
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91 =head2 new
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92
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93 Title : new
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94 Usage : my $obj = new Bio::Symbol::Alphabet();
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95 Function: Builds a new Bio::Symbol::Alphabet object
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96 Returns : Bio::Symbol::Alphabet
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97 Args : -symbols => Array ref of Bio::Symbol::SymbolI objects
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98 -subalphas=> Array ref of Bio::Symbol::AlphabetI objects
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99 representing sub alphabets
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100 =cut
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101
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102 sub new {
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103 my($class,@args) = @_;
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104
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105 my $self = $class->SUPER::new(@args);
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106 $self->{'_symbols'} = [];
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107 $self->{'_alphabets'} = [];
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108 my ($symbols, $subalphas) = $self->_rearrange([qw(SYMBOLS SUBALPHAS)],
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109 @args);
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110
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111 defined $symbols && ref($symbols) =~ /array/i && $self->symbols(@$symbols);
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112 defined $subalphas && ref($subalphas) =~ /array/i && $self->alphabets(@$subalphas);
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113 return $self;
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114 }
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115
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116 =head2 AlphabetI Interface methods
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117
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118 =cut
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119
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120 =head2 symbols
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121
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122 Title : symbols
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123 Usage : my @symbols = $alphabet->symbols();
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124 Function: Get/Set Symbol list for an alphabet
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125 List of symbols, which make up this alphabet.
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126 Returns : Array of Bio::Symbol::SymbolI objects
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127 Args : (optionalalphabets) Array of Bio::Symbol::SymbolI objects
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128
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129 =cut
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130
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131 sub symbols {
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132 my ($self,@args) = @_;
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133 if( @args ) {
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134 $self->{'_symbols'} = [];
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135 foreach my $symbol ( @args ) {
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136 if( ! defined $symbol || ! ref($symbol) ||
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137 ! $symbol->isa('Bio::Symbol::SymbolI') ) {
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138 $self->warn("Did not provide a proper Bio::Symbol::SymbolI to method 'symbols' (got $symbol)");
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139 } else {
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140 push @{$self->{'_symbols'}}, $symbol;
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141 }
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142 }
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143 }
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144 return @{$self->{'_symbols'}};
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145 }
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146
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147 =head2 alphabets
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148
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149 Title : alphabets
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150 Usage : my @alphabets = $alphabet->alphabets();
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151 Function: Get/Set Sub Alphabet list for an alphabet
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152 Sub-alphabets. E.g. codons made from DNAxDNAxDNA alphabets
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153 Returns : Array of Bio::Symbol::AlphabetI objects
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154 Args : (optional) Array of Bio::Symbol::AlphabetI objects
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155
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156 =cut
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157
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158 sub alphabets {
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159 my ($self,@args) = @_;
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160 if( @args ) {
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161 $self->{'_alphabets'} = [];
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162 foreach my $alpha ( @args ) {
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163 if( ! $alpha->isa('Bio::Symbol::AlphabetI') ) {
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164 $self->warn("Did not provide a proper Bio::Symbol::AlphabetI to method 'alphabets' (got $alpha)");
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165 } else {
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166 push @{$self->{'_alphabets'}}, $alpha;
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167 }
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168 }
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169 }
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170 return @{$self->{'_alphabets'}};
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171 }
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172
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173 =head2 contains
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174
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175 Title : contains
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176 Usage : if($alphabet->contains($symbol)) { }
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177 Function: Tests of Symbol is contained in this alphabet
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178 Returns : Boolean
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179 Args : Bio::Symbol::SymbolI
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180
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181 =cut
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182
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183 sub contains{
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184 my ($self,$testsymbol) = @_;
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185 foreach my $symbol ( $self->symbols ) {
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186 return 1 if( $symbol->equals($testsymbol) );
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187 }
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188 return 0;
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189 }
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190
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191 1;
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