Bio/DB/Expression.pm

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