Bio::DB::Expression - DESCRIPTION of Object

BioPerl documentation Contained in the BioPerl distribution.

Index

Code Index:

NAME

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Bio::DB::Expression - DESCRIPTION of Object

SYNOPSIS

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  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

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Describe the object here

FEEDBACK

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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

Support

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 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:

  https://redmine.open-bio.org/projects/bioperl/

AUTHOR - Allen Day

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Email allenday@ucla.edu

APPENDIX

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

new()

 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()

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

get_samples()

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

get_contacts()

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

get_datasets()

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

_load_expression_module

 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    :
BioPerl documentation Contained in the BioPerl distribution. 
#
# BioPerl module for Bio::DB::Expression
#
# Please direct questions and support issues to <bioperl-l@bioperl.org> 
#
# 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



# Let the code begin...


package Bio::DB::Expression;
use strict;
use base qw(Bio::Root::HTTPget Bio::Root::Root);
use Bio::Root::HTTPget;
our $DefaultSource = 'geo';


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;
}


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