Bio::Expression Platform
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Summary
Bio::Expression::Platform - DESCRIPTION of Object
Package variables
No package variables defined.
Included modules
Bio::DB::Taxonomy
Inherit
Bio::Root::Root
Synopsis
Give standard usage here
Description
Describe the object here
Methods
newDescriptionCode
_initializeDescriptionCode
get_datasetsDescriptionCode
accessionDescriptionCode
nameDescriptionCode
taxonDescriptionCode
contactDescriptionCode
dbDescriptionCode
_taxon_idDescriptionCode
taxdbDescriptionCode
Methods description
new()code    nextTop
 Usage   : my $obj = Bio::Expression::Platform->new();
Function: Builds a new Bio::Expression::Platform object
Returns : an instance of Bio::Expression::Platform
Args :
_initialize()codeprevnextTop
 Usage   : $obj->_initialize(%arg);
Function: Internal method to initialize a new Bio::Expression::Platform object
Returns : true on success
Args : passed through to new()
get_datasets()codeprevnextTop
 Usage   :
Function:
Example :
Returns :
Args :
accession()codeprevnextTop
 Usage   : $obj->accession($newval)
Function:
Example :
Returns : value of accession (a scalar)
Args : on set, new value (a scalar or undef, optional)
name()codeprevnextTop
 Usage   : $obj->name($newval)
Function:
Example :
Returns : value of name (a scalar)
Args : on set, new value (a scalar or undef, optional)
taxon()codeprevnextTop
 Usage   : $obj->taxon()
Function:
Example :
Returns : A Bio::Taxonomy::Node object
Args : none
contact()codeprevnextTop
 Usage   : $obj->contact($newval)
Function:
Example :
Returns : a Bio::Expression::Contact object
Args : on set, new value (a scalar or undef, optional)
db()codeprevnextTop
 Usage   : $obj->db($newval)
Function:
Example :
Returns : value of db (a scalar)
Args : on set, new value (a scalar or undef, optional)
_taxon_id()codeprevnextTop
 Usage   : $obj->_taxon_id($newval)
Function:
Example :
Returns : value of _taxon_id (a scalar)
Args : on set, new value (a scalar or undef, optional)
taxdb()codeprevnextTop
 Usage   : $obj->taxdb($newval)
Function:
Example :
Returns : a Bio::DB::Taxonomy object
Args : on set, new value (a scalar or undef, optional)
Methods code
newdescriptionprevnextTop
sub new {
  my($class,@args) = @_;

  my $self = $class->SUPER::new(@args);
  $self->_initialize(@args);
  return $self;
}
_initializedescriptionprevnextTop
sub _initialize {
  my($self,%arg) = @_;

  foreach my $arg (keys %arg){
    my $marg = $arg;
    $marg =~ s/^-//;
    $self->$marg($arg{$arg}) if $self->can($marg);
  }

  $self->taxdb( Bio::DB::Taxonomy->new(-source => 'entrez') );
  return 1;
}
get_datasetsdescriptionprevnextTop
sub get_datasets {
  my ($self,@args) = @_;
  my $db = $self->db();

  my @datasets = $db->get_datasets( $self );

  return @datasets;
}
accessiondescriptionprevnextTop
sub accession {
  my($self,$val) = @_;
  $self->{'accession'} = $val if defined($val);
  return $self->{'accession'};
}
namedescriptionprevnextTop
sub name {
  my($self,$val) = @_;
  $self->{'name'} = $val if defined($val);
  return $self->{'name'};
}
taxondescriptionprevnextTop
sub taxon {
  my($self) = @_;
  if ( ! $self->{'taxon'} ) {
    $self->{'taxon'} = $self->taxdb->get_Taxonomy_Node( $self->_taxon_id() );
  }
  return $self->{'taxon'};
}
contactdescriptionprevnextTop
sub contact {
  my($self,$val) = @_;
  $self->{'contact'} = $val if defined($val);
  return $self->{'contact'};
}
dbdescriptionprevnextTop
sub db {
  my($self,$val) = @_;
  $self->{'db'} = $val if defined($val);
  return $self->{'db'};
}
_taxon_iddescriptionprevnextTop
sub _taxon_id {
  my($self,$val) = @_;
  $self->{'_taxon_id'} = $val if defined($val);
  return $self->{'_taxon_id'};
}
taxdbdescriptionprevnextTop
sub taxdb {
  my($self,$val) = @_;
  $self->{'taxdb'} = $val if defined($val);
  return $self->{'taxdb'};
}



1;
}
General documentation
FEEDBACKTop
Mailing ListsTop
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
Support Top
Please direct usage questions or support issues to the mailing list:
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.
Reporting BugsTop
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/
AUTHOR - Allen DayTop
Email allenday@ucla.edu
APPENDIXTop
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _