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# $Id$
#
# BioPerl module for Bio::Expression::Platform
#
# Please direct questions and support issues to <bioperl-l@bioperl.org>
#
# Cared for by Allen Day <allenday@ucla.edu>
#
# Copyright Allen Day
#
# You may distribute this module under the same terms as perl itself
# POD documentation - main docs before the code
=head1 NAME
Bio::Expression::Platform - DESCRIPTION of Object
=head1 SYNOPSIS
Give standard usage here
=head1 DESCRIPTION
Describe the object here
=head1 FEEDBACK
=head2 Mailing Lists
User feedback is an integral part of the evolution of this and other
Bioperl modules. Send your comments and suggestions preferably to
the Bioperl mailing list. Your participation is much appreciated.
bioperl-l@bioperl.org - General discussion
http://bioperl.org/wiki/Mailing_lists - About the mailing lists
=head2 Support
Please direct usage questions or support issues to the mailing list:
I<bioperl-l@bioperl.org>
rather than to the module maintainer directly. Many experienced and
reponsive experts will be able look at the problem and quickly
address it. Please include a thorough description of the problem
with code and data examples if at all possible.
=head2 Reporting Bugs
Report bugs to the Bioperl bug tracking system to help us keep track
of the bugs and their resolution. Bug reports can be submitted via
the web:
http://bugzilla.open-bio.org/
=head1 AUTHOR - Allen Day
Email allenday@ucla.edu
=head1 APPENDIX
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _
=cut
# Let the code begin...
package Bio::Expression::Platform;
use strict;
use base qw(Bio::Root::Root);
use Bio::DB::Taxonomy;
=head2 new()
Usage : my $obj = Bio::Expression::Platform->new();
Function: Builds a new Bio::Expression::Platform object
Returns : an instance of Bio::Expression::Platform
Args :
=cut
sub new {
my($class,@args) = @_;
my $self = $class->SUPER::new(@args);
$self->_initialize(@args);
return $self;
}
=head2 _initialize()
Usage : $obj->_initialize(%arg);
Function: Internal method to initialize a new Bio::Expression::Platform object
Returns : true on success
Args : passed through to new()
=cut
sub _initialize {
my($self,%arg) = @_;
foreach my $arg (keys %arg){
my $marg = $arg;
$marg =~ s/^-//;
$self->$marg($arg{$arg}) if $self->can($marg);
}
$self->taxdb( Bio::DB::Taxonomy->new(-source => 'entrez') );
return 1;
}
=head2 get_datasets()
Usage :
Function:
Example :
Returns :
Args :
=cut
sub get_datasets {
my ($self,@args) = @_;
my $db = $self->db();
my @datasets = $db->get_datasets( $self );
return @datasets;
}
=head2 accession()
Usage : $obj->accession($newval)
Function:
Example :
Returns : value of accession (a scalar)
Args : on set, new value (a scalar or undef, optional)
=cut
sub accession {
my($self,$val) = @_;
$self->{'accession'} = $val if defined($val);
return $self->{'accession'};
}
=head2 name()
Usage : $obj->name($newval)
Function:
Example :
Returns : value of name (a scalar)
Args : on set, new value (a scalar or undef, optional)
=cut
sub name {
my($self,$val) = @_;
$self->{'name'} = $val if defined($val);
return $self->{'name'};
}
=head2 taxon()
Usage : $obj->taxon()
Function:
Example :
Returns : A Bio::Taxonomy::Node object
Args : none
=cut
sub taxon {
my($self) = @_;
if ( ! $self->{'taxon'} ) {
$self->{'taxon'} = $self->taxdb->get_Taxonomy_Node( $self->_taxon_id() );
}
return $self->{'taxon'};
}
=head2 contact()
Usage : $obj->contact($newval)
Function:
Example :
Returns : a Bio::Expression::Contact object
Args : on set, new value (a scalar or undef, optional)
=cut
sub contact {
my($self,$val) = @_;
$self->{'contact'} = $val if defined($val);
return $self->{'contact'};
}
=head2 db()
Usage : $obj->db($newval)
Function:
Example :
Returns : value of db (a scalar)
Args : on set, new value (a scalar or undef, optional)
=cut
sub db {
my($self,$val) = @_;
$self->{'db'} = $val if defined($val);
return $self->{'db'};
}
=head2 _taxon_id()
Usage : $obj->_taxon_id($newval)
Function:
Example :
Returns : value of _taxon_id (a scalar)
Args : on set, new value (a scalar or undef, optional)
=cut
sub _taxon_id {
my($self,$val) = @_;
$self->{'_taxon_id'} = $val if defined($val);
return $self->{'_taxon_id'};
}
=head2 taxdb()
Usage : $obj->taxdb($newval)
Function:
Example :
Returns : a Bio::DB::Taxonomy object
Args : on set, new value (a scalar or undef, optional)
=cut
sub taxdb {
my($self,$val) = @_;
$self->{'taxdb'} = $val if defined($val);
return $self->{'taxdb'};
}
1;