Bio/Expression/Sample.pm

   1 # $Id$
   2 #
   3 # BioPerl module for Bio::Expression::Sample
   4 #
   5 # Cared for by Allen Day <allenday@ucla.edu>
   6 #
   7 # Copyright Allen Day
   8 #
   9 # You may distribute this module under the same terms as perl itself
  10
  11 # POD documentation - main docs before the code
  12
  13 =head1 NAME
  14
  15 Bio::Expression::Sample - DESCRIPTION of Object
  16
  17 =head1 SYNOPSIS
  18
  19 Give standard usage here
  20
  21 =head1 DESCRIPTION
  22
  23 Describe the object here
  24
  25 =head1 FEEDBACK
  26
  27 =head2 Mailing Lists
  28
  29 User feedback is an integral part of the evolution of this and other
  30 Bioperl modules. Send your comments and suggestions preferably to
  31 the Bioperl mailing list.  Your participation is much appreciated.
  32
  33   bioperl-l@bioperl.org                  - General discussion
  34   http://bioperl.org/wiki/Mailing_lists  - About the mailing lists
  35
  36 =head2 Reporting Bugs
  37
  38 Report bugs to the Bioperl bug tracking system to help us keep track
  39 of the bugs and their resolution. Bug reports can be submitted via
  40 the web:
  41
  42   http://bugzilla.open-bio.org/
  43
  44 =head1 AUTHOR - Allen Day
  45
  46 Email allenday@ucla.edu
  47
  48 =head1 APPENDIX
  49
  50 The rest of the documentation details each of the object methods.
  51 Internal methods are usually preceded with a _
  52
  53 =cut
  54
  55
  56 # Let the code begin...
  57
  58
  59 package Bio::Expression::Sample;
  60 use strict;
  61 use base qw(Bio::Root::Root);
  62
  63 =head2 new()
  64
  65  Usage   : my $obj = Bio::Expression::Sample->new();
  66  Function: Builds a new Bio::Expression::Sample object
  67  Returns : an instance of Bio::Expression::Sample
  68  Args    :
  69
  70
  71 =cut
  72
  73 sub new {
  74   my($class,@args) = @_;
  75
  76   my $self = $class->SUPER::new(@args);
  77   $self->_initialize(@args);
  78   return $self;
  79 }
  80
  81 =head2 _initialize()
  82
  83  Usage   : $obj->_initialize(%arg);
  84  Function: Internal method to initialize a new Bio::Expression::Sample object
  85  Returns : true on success
  86  Args    : passed through to new()
  87
  88 =cut
  89
  90 sub _initialize {
  91   my($self,%arg) = @_;
  92
  93   foreach my $arg (keys %arg){
  94     my $marg = $arg;
  95     $marg =~ s/^-//;
  96     $self->$marg($arg{$arg}) if $self->can($marg);
  97   }
  98
  99   return 1;
 100 }
 101
 102 =head2 accession()
 103
 104  Usage   : $obj->accession($newval)
 105  Function:
 106  Example :
 107  Returns : value of accession (a scalar)
 108  Args    : on set, new value (a scalar or undef, optional)
 109
 110
 111 =cut
 112
 113 sub accession {
 114   my($self,$val) = @_;
 115   $self->{'accession'} = $val if defined($val);
 116   return $self->{'accession'};
 117 }
 118
 119 =head2 dataset()
 120
 121  Usage   : $obj->dataset($newval)
 122  Function:
 123  Example :
 124  Returns : value of dataset (a scalar)
 125  Args    : on set, new value (a scalar or undef, optional)
 126
 127
 128 =cut
 129
 130 sub dataset {
 131   my($self,$val) = @_;
 132   $self->{'dataset'} = $val if defined($val);
 133   return $self->{'dataset'};
 134 }
 135
 136 =head2 db()
 137
 138  Usage   : $obj->db($newval)
 139  Function:
 140  Example :
 141  Returns : value of db (a scalar)
 142  Args    : on set, new value (a scalar or undef, optional)
 143
 144
 145 =cut
 146
 147 sub db {
 148   my($self,$val) = @_;
 149   $self->{'db'} = $val if defined($val);
 150   return $self->{'db'};
 151 }
 152
 153
 154
 155
 156
 157
 158 =head2 name()
 159
 160  Usage   : $obj->name($newval)
 161  Function:
 162  Example :
 163  Returns : value of name (a scalar)
 164  Args    : on set, new value (a scalar or undef, optional)
 165
 166
 167 =cut
 168
 169 sub name {
 170   my($self,$val) = @_;
 171   $self->_load();
 172   $self->{'name'} = $val if defined($val);
 173   return $self->{'name'};
 174 }
 175
 176 =head2 source_name()
 177
 178  Usage   : $obj->source_name($newval)
 179  Function:
 180  Example :
 181  Returns : value of source_name (a scalar)
 182  Args    : on set, new value (a scalar or undef, optional)
 183
 184
 185 =cut
 186
 187 sub source_name {
 188   my($self,$val) = @_;
 189   $self->_load();
 190   $self->{'source_name'} = $val if defined($val);
 191   return $self->{'source_name'};
 192 }
 193
 194 =head2 description()
 195
 196  Usage   : $obj->description($newval)
 197  Function:
 198  Example :
 199  Returns : value of description (a scalar)
 200  Args    : on set, new value (a scalar or undef, optional)
 201
 202
 203 =cut
 204
 205 sub description {
 206   my($self,$val) = @_;
 207   $self->_load();
 208   $self->{'description'} = $val if defined($val);
 209   return $self->{'description'};
 210 }
 211
 212 =head2 treatment_description()
 213
 214  Usage   : $obj->treatment_description($newval)
 215  Function:
 216  Example :
 217  Returns : value of treatment_description (a scalar)
 218  Args    : on set, new value (a scalar or undef, optional)
 219
 220
 221 =cut
 222
 223 sub treatment_description {
 224   my($self,$val) = @_;
 225   $self->_load();
 226   $self->{'treatment_description'} = $val if defined($val);
 227   return $self->{'treatment_description'};
 228 }
 229
 230 sub _load {
 231   my $self = shift;
 232   if ( $self->{'_load'} ) {
 233     return 1;
 234   }
 235   $self->{'_load'}++;
 236   $self->db->fill_sample( $self );
 237   return $self->{'_load'};
 238 }
 239
 240 1;