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Summary

Bio::DB::Expression - DESCRIPTION of Object

Package variables

Included modules

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

Methods description

 Usage   : my $obj = Bio::DB::Expression->new();
 Function: Builds a new Bio::DB::Expression object 
 Returns : an instance of Bio::DB::Expression
 Args    :

 Usage   :
 Function:
 Example :
 Returns : a list of Bio::Expression::Platform objects
 Args    :

 Usage   :
 Function:
 Example :
 Returns : a list of Bio::Expression::Sample objects
 Args    :

 Usage   :
 Function:
 Example :
 Returns : a list of Bio::Expression::Contact objects
 Args    :

 Usage   :
 Function:
 Example :
 Returns : a list of Bio::Expression::DataSet objects
 Args    :

 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

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);
  }

}

sub get_platforms {

  my ($self,@args) = @_;
  $self->throw_not_implemented();

}

sub get_samples {

  my ($self,@args) = @_;
  $self->throw_not_implemented();

}

sub get_contacts {

  my ($self,@args) = @_;
  $self->throw_not_implemented();

}

sub get_datasets {

  my ($self,@args) = @_;
  $self->throw_not_implemented();

}

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

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

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.

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/

Email allenday@ucla.edu

The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _