—
—
—
—
—
—
—
—
—
—
—

              
# $Id: Platform.pm,v 1.4.4.1 2006/10/02 23:10:17 sendu Exp $
#
# BioPerl module for Bio::Expression::Platform
#
# 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
HideShow 42 lines of Pod
=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 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;
HideShow 9 lines of Pod
=head2 new()
 Usage   : my $obj = new Bio::Expression::Platform();
 Function: Builds a new Bio::Expression::Platform object 
 Returns : an instance of Bio::Expression::Platform
 Args    :
=cut
sub new {
  my($class,@args) = @_;
  my $self = $class->SUPER::new(@args);
  $self->_initialize(@args);
  return $self;
}
HideShow 9 lines of Pod
=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);
  }
  $self->taxdb( Bio::DB::Taxonomy->new(-source => 'entrez') );
  return 1;
}
HideShow 10 lines of Pod
=head2 get_datasets()
 Usage   :
 Function:
 Example :
 Returns : 
 Args    :
=cut
sub get_datasets {
  my ($self,@args) = @_;
  my $db = $self->db();
  my @datasets = $db->get_datasets( $self );
  return @datasets;
}
HideShow 11 lines of Pod
=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'};
}
HideShow 11 lines of Pod
=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'};
}
HideShow 11 lines of Pod
=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'};
}
HideShow 11 lines of Pod
=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'};
}
HideShow 11 lines of Pod
=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'};
}
HideShow 11 lines of Pod
=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'};
}
HideShow 11 lines of Pod
=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;