branch-1-6/Bio/Expression/Sample.pm

   1 # $Id$
   2 #
   3 # BioPerl module for Bio::Expression::Sample
   4 #
   5 # Please direct questions and support issues to <bioperl-l@bioperl.org>
   6 #
   7 # Cared for by Allen Day <allenday@ucla.edu>
   8 #
   9 # Copyright Allen Day
  10 #
  11 # You may distribute this module under the same terms as perl itself
  12
  13 # POD documentation - main docs before the code
  14
  15 =head1 NAME
  16
  17 Bio::Expression::Sample - DESCRIPTION of Object
  18
  19 =head1 SYNOPSIS
  20
  21 Give standard usage here
  22
  23 =head1 DESCRIPTION
  24
  25 Describe the object here
  26
  27 =head1 FEEDBACK
  28
  29 =head2 Mailing Lists
  30
  31 User feedback is an integral part of the evolution of this and other
  32 Bioperl modules. Send your comments and suggestions preferably to
  33 the Bioperl mailing list.  Your participation is much appreciated.
  34
  35   bioperl-l@bioperl.org                  - General discussion
  36   http://bioperl.org/wiki/Mailing_lists  - About the mailing lists
  37
  38 =head2 Support
  39
  40 Please direct usage questions or support issues to the mailing list:
  41
  42 I<bioperl-l@bioperl.org>
  43
  44 rather than to the module maintainer directly. Many experienced and
  45 reponsive experts will be able look at the problem and quickly
  46 address it. Please include a thorough description of the problem
  47 with code and data examples if at all possible.
  48
  49 =head2 Reporting Bugs
  50
  51 Report bugs to the Bioperl bug tracking system to help us keep track
  52 of the bugs and their resolution. Bug reports can be submitted via
  53 the web:
  54
  55   http://bugzilla.open-bio.org/
  56
  57 =head1 AUTHOR - Allen Day
  58
  59 Email allenday@ucla.edu
  60
  61 =head1 APPENDIX
  62
  63 The rest of the documentation details each of the object methods.
  64 Internal methods are usually preceded with a _
  65
  66 =cut
  67
  68
  69 # Let the code begin...
  70
  71
  72 package Bio::Expression::Sample;
  73 use strict;
  74 use base qw(Bio::Root::Root);
  75
  76 =head2 new()
  77
  78  Usage   : my $obj = Bio::Expression::Sample->new();
  79  Function: Builds a new Bio::Expression::Sample object
  80  Returns : an instance of Bio::Expression::Sample
  81  Args    :
  82
  83
  84 =cut
  85
  86 sub new {
  87   my($class,@args) = @_;
  88
  89   my $self = $class->SUPER::new(@args);
  90   $self->_initialize(@args);
  91   return $self;
  92 }
  93
  94 =head2 _initialize()
  95
  96  Usage   : $obj->_initialize(%arg);
  97  Function: Internal method to initialize a new Bio::Expression::Sample object
  98  Returns : true on success
  99  Args    : passed through to new()
 100
 101 =cut
 102
 103 sub _initialize {
 104   my($self,%arg) = @_;
 105
 106   foreach my $arg (keys %arg){
 107     my $marg = $arg;
 108     $marg =~ s/^-//;
 109     $self->$marg($arg{$arg}) if $self->can($marg);
 110   }
 111
 112   return 1;
 113 }
 114
 115 =head2 accession()
 116
 117  Usage   : $obj->accession($newval)
 118  Function:
 119  Example :
 120  Returns : value of accession (a scalar)
 121  Args    : on set, new value (a scalar or undef, optional)
 122
 123
 124 =cut
 125
 126 sub accession {
 127   my($self,$val) = @_;
 128   $self->{'accession'} = $val if defined($val);
 129   return $self->{'accession'};
 130 }
 131
 132 =head2 dataset()
 133
 134  Usage   : $obj->dataset($newval)
 135  Function:
 136  Example :
 137  Returns : value of dataset (a scalar)
 138  Args    : on set, new value (a scalar or undef, optional)
 139
 140
 141 =cut
 142
 143 sub dataset {
 144   my($self,$val) = @_;
 145   $self->{'dataset'} = $val if defined($val);
 146   return $self->{'dataset'};
 147 }
 148
 149 =head2 db()
 150
 151  Usage   : $obj->db($newval)
 152  Function:
 153  Example :
 154  Returns : value of db (a scalar)
 155  Args    : on set, new value (a scalar or undef, optional)
 156
 157
 158 =cut
 159
 160 sub db {
 161   my($self,$val) = @_;
 162   $self->{'db'} = $val if defined($val);
 163   return $self->{'db'};
 164 }
 165
 166
 167
 168
 169
 170
 171 =head2 name()
 172
 173  Usage   : $obj->name($newval)
 174  Function:
 175  Example :
 176  Returns : value of name (a scalar)
 177  Args    : on set, new value (a scalar or undef, optional)
 178
 179
 180 =cut
 181
 182 sub name {
 183   my($self,$val) = @_;
 184   $self->_load();
 185   $self->{'name'} = $val if defined($val);
 186   return $self->{'name'};
 187 }
 188
 189 =head2 source_name()
 190
 191  Usage   : $obj->source_name($newval)
 192  Function:
 193  Example :
 194  Returns : value of source_name (a scalar)
 195  Args    : on set, new value (a scalar or undef, optional)
 196
 197
 198 =cut
 199
 200 sub source_name {
 201   my($self,$val) = @_;
 202   $self->_load();
 203   $self->{'source_name'} = $val if defined($val);
 204   return $self->{'source_name'};
 205 }
 206
 207 =head2 description()
 208
 209  Usage   : $obj->description($newval)
 210  Function:
 211  Example :
 212  Returns : value of description (a scalar)
 213  Args    : on set, new value (a scalar or undef, optional)
 214
 215
 216 =cut
 217
 218 sub description {
 219   my($self,$val) = @_;
 220   $self->_load();
 221   $self->{'description'} = $val if defined($val);
 222   return $self->{'description'};
 223 }
 224
 225 =head2 treatment_description()
 226
 227  Usage   : $obj->treatment_description($newval)
 228  Function:
 229  Example :
 230  Returns : value of treatment_description (a scalar)
 231  Args    : on set, new value (a scalar or undef, optional)
 232
 233
 234 =cut
 235
 236 sub treatment_description {
 237   my($self,$val) = @_;
 238   $self->_load();
 239   $self->{'treatment_description'} = $val if defined($val);
 240   return $self->{'treatment_description'};
 241 }
 242
 243 sub _load {
 244   my $self = shift;
 245   if ( $self->{'_load'} ) {
 246     return 1;
 247   }
 248   $self->{'_load'}++;
 249   $self->db->fill_sample( $self );
 250   return $self->{'_load'};
 251 }
 252
 253 1;