Bio/DB/Expression.pm

   1 # $Id$
   2 #
   3 # BioPerl module for Bio::DB::Expression
   4 #
   5 # Please direct questions and support issues to <bioperl-l@bioperl.org>
   6 #
   7 # Cared for by Allen Day <allenday@ucla.edu>
   8 #
   9 # Copyright Allen Day
  10 #
  11 # You may distribute this module under the same terms as perl itself
  12
  13 # POD documentation - main docs before the code
  14
  15 =head1 NAME
  16
  17 Bio::DB::Expression - DESCRIPTION of Object
  18
  19 =head1 SYNOPSIS
  20
  21   use Bio::DB::Expression;
  22   my $db = Bio::DB::Expression->new( -source => 'geo' );
  23   my @platforms = $db->get_platforms();
  24   foreach my $platform ( @platforms ) {
  25     my @datasets = $platform->get_datasets();
  26     foreach my $dataset ( @datasets ) {
  27       my @samples = $dataset->get_samples();
  28       foreach my $sample ( @samples ) {
  29         #...
  30       }
  31     }
  32   }
  33
  34 =head1 DESCRIPTION
  35
  36 Describe the object here
  37
  38 =head1 FEEDBACK
  39
  40 =head2 Mailing Lists
  41
  42 User feedback is an integral part of the evolution of this and other
  43 Bioperl modules. Send your comments and suggestions preferably to
  44 the Bioperl mailing list.  Your participation is much appreciated.
  45
  46   bioperl-l@bioperl.org                  - General discussion
  47   http://bioperl.org/wiki/Mailing_lists  - About the mailing lists
  48
  49 =head2 Support
  50
  51 Please direct usage questions or support issues to the mailing list:
  52
  53 L<bioperl-l@bioperl.org>
  54
  55 rather than to the module maintainer directly. Many experienced and
  56 reponsive experts will be able look at the problem and quickly
  57 address it. Please include a thorough description of the problem
  58 with code and data examples if at all possible.
  59
  60 =head2 Reporting Bugs
  61
  62 Report bugs to the Bioperl bug tracking system to help us keep track
  63 of the bugs and their resolution. Bug reports can be submitted via
  64 the web:
  65
  66   http://bugzilla.open-bio.org/
  67
  68 =head1 AUTHOR - Allen Day
  69
  70 Email allenday@ucla.edu
  71
  72 =head1 APPENDIX
  73
  74 The rest of the documentation details each of the object methods.
  75 Internal methods are usually preceded with a _
  76
  77 =cut
  78
  79
  80 # Let the code begin...
  81
  82
  83 package Bio::DB::Expression;
  84 use strict;
  85 use base qw(Bio::Root::HTTPget Bio::Root::Root);
  86 use Bio::Root::HTTPget;
  87 our $DefaultSource = 'geo';
  88
  89 =head2 new()
  90
  91  Usage   : my $obj = Bio::DB::Expression->new();
  92  Function: Builds a new Bio::DB::Expression object
  93  Returns : an instance of Bio::DB::Expression
  94  Args    :
  95
  96
  97 =cut
  98
  99 sub new {
 100   my($class,@args) = @_;
 101
 102   if( $class =~ /Bio::DB::Expression::(\S+)/ ) {
 103     my ($self) = $class->SUPER::new(@args);
 104     $self->_initialize(@args);
 105     return $self;
 106   } else {
 107     my %param = @args;
 108     @param{ map { lc $_ } keys %param } = values %param; # lowercase keys
 109     my $source = $param{'-source'} || $DefaultSource;
 110
 111     $source = "\L$source";      # normalize capitalization to lower case
 112
 113     # normalize capitalization
 114     return unless( $class->_load_expression_module($source) );
 115     return "Bio::DB::Expression::$source"->new(@args);
 116   }
 117 }
 118
 119 =head2 get_platforms()
 120
 121  Usage   :
 122  Function:
 123  Example :
 124  Returns : a list of Bio::Expression::Platform objects
 125  Args    :
 126
 127 =cut
 128
 129 sub get_platforms {
 130   my ($self,@args) = @_;
 131   $self->throw_not_implemented();
 132 }
 133
 134 =head2 get_samples()
 135
 136  Usage   :
 137  Function:
 138  Example :
 139  Returns : a list of Bio::Expression::Sample objects
 140  Args    :
 141
 142 =cut
 143
 144 sub get_samples {
 145   my ($self,@args) = @_;
 146   $self->throw_not_implemented();
 147 }
 148
 149 =head2 get_contacts()
 150
 151  Usage   :
 152  Function:
 153  Example :
 154  Returns : a list of Bio::Expression::Contact objects
 155  Args    :
 156
 157 =cut
 158
 159 sub get_contacts {
 160   my ($self,@args) = @_;
 161   $self->throw_not_implemented();
 162 }
 163
 164 =head2 get_datasets()
 165
 166  Usage   :
 167  Function:
 168  Example :
 169  Returns : a list of Bio::Expression::DataSet objects
 170  Args    :
 171
 172 =cut
 173
 174 sub get_datasets {
 175   my ($self,@args) = @_;
 176   $self->throw_not_implemented();
 177 }
 178
 179
 180
 181
 182 =head2 _load_expression_module
 183
 184  Title   : _load_expression_module
 185  Usage   : *INTERNAL Bio::DB::Expression stuff*
 186  Function: Loads up (like use) a module at run time on demand
 187  Example :
 188  Returns :
 189  Args    :
 190
 191 =cut
 192
 193 sub _load_expression_module {
 194     my ($self, $source) = @_;
 195     my $module = "Bio::DB::Expression::" . $source;
 196     my $ok;
 197
 198     eval { $ok = $self->_load_module($module) };
 199     if ( $@ ) {
 200         print STDERR $@;
 201         print STDERR <<END;
 202 $self: $source cannot be found
 203 Exception $@
 204 For more information about the Bio::DB::Expression system please see
 205 the Bio::DB::Expression docs.  This includes ways of checking for
 206 formats at compile time, not run time.
 207 END
 208   ;
 209     }
 210     return $ok;
 211 }
 212
 213
 214 1;