Bio/DB/GFF/Featname.pm

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