Bio/Expression/Platform.pm

   1 # $Id$
   2 #
   3 # BioPerl module for Bio::Expression::Platform
   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::Platform - 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::Platform;
  60 use strict;
  61 use base qw(Bio::Root::Root);
  62 use Bio::DB::Taxonomy;
  63
  64 =head2 new()
  65
  66  Usage   : my $obj = Bio::Expression::Platform->new();
  67  Function: Builds a new Bio::Expression::Platform object
  68  Returns : an instance of Bio::Expression::Platform
  69  Args    :
  70
  71 =cut
  72
  73 sub new {
  74   my($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   : $obj->_initialize(%arg);
  84  Function: Internal method to initialize a new Bio::Expression::Platform object
  85  Returns : true on success
  86  Args    : passed through to new()
  87
  88 =cut
  89
  90 sub _initialize {
  91   my($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   $self->taxdb( Bio::DB::Taxonomy->new(-source => 'entrez') );
 100   return 1;
 101 }
 102
 103
 104
 105 =head2 get_datasets()
 106
 107  Usage   :
 108  Function:
 109  Example :
 110  Returns :
 111  Args    :
 112
 113 =cut
 114
 115 sub get_datasets {
 116   my ($self,@args) = @_;
 117   my $db = $self->db();
 118
 119   my @datasets = $db->get_datasets( $self );
 120
 121   return @datasets;
 122 }
 123
 124 =head2 accession()
 125
 126  Usage   : $obj->accession($newval)
 127  Function:
 128  Example :
 129  Returns : value of accession (a scalar)
 130  Args    : on set, new value (a scalar or undef, optional)
 131
 132
 133 =cut
 134
 135 sub accession {
 136   my($self,$val) = @_;
 137   $self->{'accession'} = $val if defined($val);
 138   return $self->{'accession'};
 139 }
 140
 141 =head2 name()
 142
 143  Usage   : $obj->name($newval)
 144  Function:
 145  Example :
 146  Returns : value of name (a scalar)
 147  Args    : on set, new value (a scalar or undef, optional)
 148
 149
 150 =cut
 151
 152 sub name {
 153   my($self,$val) = @_;
 154   $self->{'name'} = $val if defined($val);
 155   return $self->{'name'};
 156 }
 157
 158 =head2 taxon()
 159
 160  Usage   : $obj->taxon()
 161  Function:
 162  Example :
 163  Returns : A Bio::Taxonomy::Node object
 164  Args    : none
 165
 166
 167 =cut
 168
 169 sub taxon {
 170   my($self) = @_;
 171   if ( ! $self->{'taxon'} ) {
 172     $self->{'taxon'} = $self->taxdb->get_Taxonomy_Node( $self->_taxon_id() );
 173   }
 174   return $self->{'taxon'};
 175 }
 176
 177 =head2 contact()
 178
 179  Usage   : $obj->contact($newval)
 180  Function:
 181  Example :
 182  Returns : a Bio::Expression::Contact object
 183  Args    : on set, new value (a scalar or undef, optional)
 184
 185
 186 =cut
 187
 188 sub contact {
 189   my($self,$val) = @_;
 190   $self->{'contact'} = $val if defined($val);
 191   return $self->{'contact'};
 192 }
 193
 194 =head2 db()
 195
 196  Usage   : $obj->db($newval)
 197  Function:
 198  Example :
 199  Returns : value of db (a scalar)
 200  Args    : on set, new value (a scalar or undef, optional)
 201
 202
 203 =cut
 204
 205 sub db {
 206   my($self,$val) = @_;
 207   $self->{'db'} = $val if defined($val);
 208   return $self->{'db'};
 209 }
 210
 211 =head2 _taxon_id()
 212
 213  Usage   : $obj->_taxon_id($newval)
 214  Function:
 215  Example :
 216  Returns : value of _taxon_id (a scalar)
 217  Args    : on set, new value (a scalar or undef, optional)
 218
 219
 220 =cut
 221
 222 sub _taxon_id {
 223   my($self,$val) = @_;
 224   $self->{'_taxon_id'} = $val if defined($val);
 225   return $self->{'_taxon_id'};
 226 }
 227
 228 =head2 taxdb()
 229
 230  Usage   : $obj->taxdb($newval)
 231  Function:
 232  Example :
 233  Returns : a Bio::DB::Taxonomy object
 234  Args    : on set, new value (a scalar or undef, optional)
 235
 236
 237 =cut
 238
 239 sub taxdb {
 240   my($self,$val) = @_;
 241   $self->{'taxdb'} = $val if defined($val);
 242   return $self->{'taxdb'};
 243 }
 244
 245
 246
 247 1;