3 # BioPerl module for Bio::Expression::Platform
5 # Cared for by Allen Day <allenday@ucla.edu>
9 # You may distribute this module under the same terms as perl itself
11 # POD documentation - main docs before the code
15 Bio::Expression::Platform - DESCRIPTION of Object
19 Give standard usage here
23 Describe the object here
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.
33 bioperl-l@bioperl.org - General discussion
34 http://bioperl.org/wiki/Mailing_lists - About the mailing lists
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
42 http://bugzilla.open-bio.org/
44 =head1 AUTHOR - Allen Day
46 Email allenday@ucla.edu
50 The rest of the documentation details each of the object methods.
51 Internal methods are usually preceded with a _
56 # Let the code begin...
59 package Bio
::Expression
::Platform
;
61 use base
qw(Bio::Root::Root);
62 use Bio
::DB
::Taxonomy
;
66 Usage : my $obj = Bio::Expression::Platform->new();
67 Function: Builds a new Bio::Expression::Platform object
68 Returns : an instance of Bio::Expression::Platform
74 my($class,@args) = @_;
76 my $self = $class->SUPER::new
(@args);
77 $self->_initialize(@args);
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()
93 foreach my $arg (keys %arg){
96 $self->$marg($arg{$arg}) if $self->can($marg);
99 $self->taxdb( Bio
::DB
::Taxonomy
->new(-source
=> 'entrez') );
105 =head2 get_datasets()
116 my ($self,@args) = @_;
117 my $db = $self->db();
119 my @datasets = $db->get_datasets( $self );
126 Usage : $obj->accession($newval)
129 Returns : value of accession (a scalar)
130 Args : on set, new value (a scalar or undef, optional)
137 $self->{'accession'} = $val if defined($val);
138 return $self->{'accession'};
143 Usage : $obj->name($newval)
146 Returns : value of name (a scalar)
147 Args : on set, new value (a scalar or undef, optional)
154 $self->{'name'} = $val if defined($val);
155 return $self->{'name'};
160 Usage : $obj->taxon()
163 Returns : A Bio::Taxonomy::Node object
171 if ( ! $self->{'taxon'} ) {
172 $self->{'taxon'} = $self->taxdb->get_Taxonomy_Node( $self->_taxon_id() );
174 return $self->{'taxon'};
179 Usage : $obj->contact($newval)
182 Returns : a Bio::Expression::Contact object
183 Args : on set, new value (a scalar or undef, optional)
190 $self->{'contact'} = $val if defined($val);
191 return $self->{'contact'};
196 Usage : $obj->db($newval)
199 Returns : value of db (a scalar)
200 Args : on set, new value (a scalar or undef, optional)
207 $self->{'db'} = $val if defined($val);
208 return $self->{'db'};
213 Usage : $obj->_taxon_id($newval)
216 Returns : value of _taxon_id (a scalar)
217 Args : on set, new value (a scalar or undef, optional)
224 $self->{'_taxon_id'} = $val if defined($val);
225 return $self->{'_taxon_id'};
230 Usage : $obj->taxdb($newval)
233 Returns : a Bio::DB::Taxonomy object
234 Args : on set, new value (a scalar or undef, optional)
241 $self->{'taxdb'} = $val if defined($val);
242 return $self->{'taxdb'};