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1 =head1 NAME
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2
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3 Bio::DB::GFF::Featname -- The name of a feature
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4
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5 =head1 SYNOPSIS
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6
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7 use Bio::DB::GFF;
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8
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9 my $db = Bio::DB::GFF->new( -adaptor => 'dbi:mysql',
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10 -dsn => 'dbi:mysql:elegans42');
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11
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12 my $feature = Bio::DB::GFF::Featname->new(Locus => 'unc-19');
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13 my $segment = $db->segment($feature);
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14
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15 =head1 DESCRIPTION
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16
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17 Bio::DB::GFF::Featname is the name of a feature. It contains two
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18 fields: name and class. It is typically used by the Bio::DB::GFF
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19 module to denote a group, and is accepted by
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20 Bio::DB::Relsegment-E<gt>new() and Bio::DB::GFF-E<gt>segment() as a
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21 replacement for the -name and -class arguments.
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22
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23 =head1 METHODS
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24
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25 =cut
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26
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27 package Bio::DB::GFF::Featname;
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28 use strict;
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29 use vars '@ISA';
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30 use Bio::Root::RootI;
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31 @ISA = qw(Bio::Root::RootI);
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32
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33 use overload
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34 '""' => 'asString',
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35 fallback => 1;
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36
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37 =head2 new
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38
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39 Title : new
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40 Usage : $name = Bio::DB::GFF::Featname->new($class,$name)
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41 Function: create a new Bio::DB::GFF::Featname object
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42 Returns : a new Bio::DB::GFF::Featname object
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43 Args : class and ID
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44 Status : Public
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45
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46 =cut
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47
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48 sub new {
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49 # use a blessed array for speed
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50 my $pack = shift;
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51 bless [@_],$pack; # class,name
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52 }
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53
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54 sub _cleanup_methods { return; }
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55
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56 =head2 id
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57
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58 Title : id
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59 Usage : $id = $name->id
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60 Function: return a unique ID for the combination of class and name
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61 Returns : a string
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62 Args : none
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63 Status : Public
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64
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65 This method returns a unique combination of the name and class in the
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66 form "class:name". Coincidentally, this is the same format used
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67 by AceDB.
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68
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69 =cut
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70
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71 sub id {
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72 my $self = shift;
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73 return join ':',@$self;
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74 }
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75
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76 =head2 name
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77
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78 Title : name
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79 Usage : $name = $name->name
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80 Function: return the name of the Featname
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81 Returns : a string
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82 Args : none
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83 Status : Public
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84
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85 =cut
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86
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87 sub name { shift->[1] }
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88
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89 =head2 class
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90
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91 Title : class
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92 Usage : $class = $name->class
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93 Function: return the name of the Featname
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94 Returns : a string
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95 Args : none
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96 Status : Public
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97
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98 =cut
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99
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100 sub class { shift->[0] }
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101
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102 =head2 asString
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103
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104 Title : asString
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105 Usage : $string = $name->asString
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106 Function: same as name()
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107 Returns : a string
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108 Args : none
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109 Status : Public
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110
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111 This method is used to overload the "" operator. It is equivalent to
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112 calling name().
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113
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114 =cut
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115
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116 sub asString { shift->name }
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117
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118 =head2 clone
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119
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120 Title : clone
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121 Usage : $new_clone = $type->clone;
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122 Function: clone this object
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123 Returns : a new Bio::DB::GFF::Featname object
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124 Args : none
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125 Status : Public
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126
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127 This method creates an exact copy of the object.
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128
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129 =cut
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130
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131 sub clone {
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132 my $self = shift;
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133 return bless [@$self],ref $self;
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134 }
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135
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136 =head1 BUGS
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137
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138 This module is still under development.
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139
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140 =head1 SEE ALSO
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141
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142 L<bioperl>, L<Bio::DB::GFF>, L<Bio::DB::RelSegment>
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143
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144 =head1 AUTHOR
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145
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146 Lincoln Stein E<lt>lstein@cshl.orgE<gt>.
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147
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148 Copyright (c) 2001 Cold Spring Harbor Laboratory.
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149
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150 This library is free software; you can redistribute it and/or modify
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151 it under the same terms as Perl itself.
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152
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153 =cut
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154
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155 1;
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