Bio/DB/SeqVersion.pm

   1 #
   2 # BioPerl module for Bio::DB::SeqVersion
   3 #
   4 # Please direct questions and support issues to <bioperl-l@bioperl.org>
   5 #
   6 # Cared for by Brian Osborne
   7 #
   8 # Copyright Brian Osborne 2006
   9 #
  10 # You may distribute this module under the same terms as Perl itself
  11 #
  12 # POD documentation - main docs before the code
  13
  14 =head1 NAME
  15
  16 Bio::DB::SeqVersion - front end to querying databases for identifier
  17 versions
  18
  19 =head1 SYNOPSIS
  20
  21   use Bio::DB::SeqVersion;
  22
  23   my $query = Bio::DB::SeqVersion->new(-type => 'gi');
  24
  25   my @all_gis = $query->get_all(2);
  26
  27   my $live_gi = $query->get_recent(2);
  28
  29 =head1 DESCRIPTION
  30
  31 The default type is 'gi'.
  32
  33 =head1 FEEDBACK
  34
  35 =head2 Mailing Lists
  36
  37 User feedback is an integral part of the evolution of this and other
  38 Bioperl modules. Send your comments and suggestions preferably to
  39 the Bioperl mailing list.  Your participation is much appreciated.
  40
  41   bioperl-l@bioperl.org                  - General discussion
  42   http://bioperl.org/wiki/Mailing_lists  - About the mailing lists
  43
  44 =head2 Support
  45
  46 Please direct usage questions or support issues to the mailing list:
  47
  48 I<bioperl-l@bioperl.org>
  49
  50 rather than to the module maintainer directly. Many experienced and
  51 reponsive experts will be able look at the problem and quickly
  52 address it. Please include a thorough description of the problem
  53 with code and data examples if at all possible.
  54
  55 =head2 Reporting Bugs
  56
  57 Report bugs to the Bioperl bug tracking system to help us keep track
  58 of the bugs and their resolution. Bug reports can be submitted via
  59 the web:
  60
  61   https://github.com/bioperl/bioperl-live/issues
  62
  63 =head1 AUTHOR - Brian Osborne
  64
  65 Email bosborne at alum.mit.edu
  66
  67 =head1 CONTRIBUTORS
  68
  69 Torsten Seemann - torsten.seemann AT infotech.monash.edu.au
  70
  71 =head1 APPENDIX
  72
  73 The rest of the documentation details each of the object methods.
  74 Internal methods are usually preceded with a _
  75
  76 =cut
  77
  78 # Let the code begin...
  79
  80 package Bio::DB::SeqVersion;
  81 use strict;
  82
  83 use base qw(Bio::WebAgent Bio::Root::Root);
  84
  85 # Private class variable
  86
  87 my $DEFAULTIDTYPE = 'gi'; # sub default_id_type()
  88
  89 =head2 new()
  90
  91  Usage   : my $obj = Bio::DB::SeqVersion->new();
  92  Function: Create a Bio::DB::SeqVersion object
  93  Returns : An instance of Bio::DB::SeqVersion
  94  Args    : -type      Identifier namespace, default is 'gi'
  95
  96 =cut
  97
  98 sub new {
  99   my($class,@args) = @_;
 100
 101   if( $class =~ /Bio::DB::SeqVersion::\S+/ ) {
 102     my ($self) = $class->SUPER::new(@args);
 103     $self->_initialize(@args);
 104     return $self;
 105   }
 106   else {
 107     my %param = @args;
 108     @param{ map { lc $_ } keys %param } = values %param; # lowercase keys
 109
 110     # we delete '-type' so it doesn't get passed to the sub-class constructor
 111     # note: delete() returns the value of the item deleted (undef if non-existent)
 112     my $type = lc( delete($param{'-type'}) || $DEFAULTIDTYPE );
 113
 114     return unless( $class->_load_seqversion_module($type) );
 115
 116     # we pass %param here, not @args, as we have filtered out -type
 117     return "Bio::DB::SeqVersion::$type"->new(%param);
 118   }
 119 }
 120
 121 =head2 get_recent()
 122
 123  Usage   :
 124  Function:
 125  Example :
 126  Returns :
 127  Args    :
 128
 129 =cut
 130
 131 sub get_recent {
 132   my ($self,@args) = @_;
 133   $self->throw_not_implemented();
 134 }
 135
 136 =head2 get_all()
 137
 138  Usage   :
 139  Function:
 140  Example :
 141  Returns :
 142  Args    :
 143
 144 =cut
 145
 146 sub get_all {
 147         my ($self,@args) = @_;
 148         $self->throw_not_implemented();
 149 }
 150
 151 =head2 _load_seqversion_module
 152
 153  Title   : _load_seqversion_module
 154  Usage   : Used internally
 155  Function: Loads up a module at run time on demand
 156  Example :
 157  Returns :
 158  Args    : Name of identifier type
 159
 160 =cut
 161
 162 sub _load_seqversion_module {
 163         my ($self,$db) = @_;
 164         my $module = "Bio::DB::SeqVersion::" . $db;
 165         my $ok;
 166
 167         eval { $ok = $self->_load_module($module) };
 168         if ( $@ ) {
 169                 print STDERR $@;
 170                 print STDERR <<END;
 171 $self: $module cannot be found
 172 Exception $@
 173 For more information about the Bio::DB::SeqVersion system please see
 174 the Bio::DB::SeqVersion docs.
 175 END
 176                 ;
 177         }
 178         return $ok;
 179 }
 180
 181 =head2 default_id_type
 182
 183  Title   : default_id_type
 184  Usage   : my $type = $self->default_id_type
 185  Function: Returns default identifier type for this module
 186  Returns : string
 187  Args    : none
 188
 189 =cut
 190
 191 sub default_id_type {
 192     return $DEFAULTIDTYPE;
 193 }
 194
 195 1;