Bio::DB Expression
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Summary
Bio::DB::Expression - DESCRIPTION of Object
Package variables
No package variables defined.
Included modules
Bio::Root::HTTPget
Inherit
Bio::Root::HTTPget Bio::Root::Root
Synopsis
  use Bio::DB::Expression;
my $db = Bio::DB::Expression->new( -source => 'geo' );
my @platforms = $db->get_platforms();
foreach my $platform ( @platforms ) {
my @datasets = $platform->get_datasets();
foreach my $dataset ( @datasets ) {
my @samples = $dataset->get_samples();
foreach my $sample ( @samples ) {
#...
}
}
}
Description
Describe the object here
Methods
newDescriptionCode
get_platformsDescriptionCode
get_samplesDescriptionCode
get_contactsDescriptionCode
get_datasetsDescriptionCode
_load_expression_moduleDescriptionCode
Methods description
new()code    nextTop
 Usage   : my $obj = Bio::DB::Expression->new();
Function: Builds a new Bio::DB::Expression object
Returns : an instance of Bio::DB::Expression
Args :
get_platforms()codeprevnextTop
 Usage   :
Function:
Example :
Returns : a list of Bio::Expression::Platform objects
Args :
get_samples()codeprevnextTop
 Usage   :
Function:
Example :
Returns : a list of Bio::Expression::Sample objects
Args :
get_contacts()codeprevnextTop
 Usage   :
Function:
Example :
Returns : a list of Bio::Expression::Contact objects
Args :
get_datasets()codeprevnextTop
 Usage   :
Function:
Example :
Returns : a list of Bio::Expression::DataSet objects
Args :
_load_expression_modulecodeprevnextTop
 Title   : _load_expression_module
Usage : *INTERNAL Bio::DB::Expression stuff*
Function: Loads up (like use) a module at run time on demand
Example :
Returns :
Args :
Methods code
newdescriptionprevnextTop
sub new {
  my($class,@args) = @_;

  if( $class =~ /Bio::DB::Expression::(\S+)/ ) {
    my ($self) = $class->SUPER::new(@args);
    $self->_initialize(@args);
    return $self;
  } else {
    my %param = @args;
    @param{ map { lc $_ } keys %param } = values %param; # lowercase keys
my $source = $param{'-source'} || $DefaultSource; $source = "\L$source"; # normalize capitalization to lower case
# normalize capitalization
return unless( $class->_load_expression_module($source) ); return "Bio::DB::Expression::$source"->new(@args); }
}
get_platformsdescriptionprevnextTop
sub get_platforms {
  my ($self,@args) = @_;
  $self->throw_not_implemented();
}
get_samplesdescriptionprevnextTop
sub get_samples {
  my ($self,@args) = @_;
  $self->throw_not_implemented();
}
get_contactsdescriptionprevnextTop
sub get_contacts {
  my ($self,@args) = @_;
  $self->throw_not_implemented();
}
get_datasetsdescriptionprevnextTop
sub get_datasets {
  my ($self,@args) = @_;
  $self->throw_not_implemented();
}
_load_expression_moduledescriptionprevnextTop
sub _load_expression_module {
    my ($self, $source) = @_;
    my $module = "Bio::DB::Expression::" . $source;
    my $ok;

    eval { $ok = $self->_load_module($module) };
    if ( $@ ) {
	print STDERR $@;
	print STDERR <<END;
$self: $source cannot be found
Exception $@
For more information about the Bio::DB::Expression system please see
the Bio::DB::Expression docs. This includes ways of checking for
formats at compile time, not run time.
END
; } return $ok; } 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:
  https://redmine.open-bio.org/projects/bioperl/
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 _