———————————# $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
=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:
=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
Bio::DB::Taxonomy;
=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
;
}
=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;