Bio/DB/RandomAccessI.pm

   1 # POD documentation - main docs before the code
   2 #
   3 #
   4
   5 =head1 NAME
   6
   7 Bio::DB::RandomAccessI - Abstract interface for a sequence database
   8
   9 =head1 SYNOPSIS
  10
  11   #
  12   # get a database object somehow using a concrete class
  13   #
  14
  15   $seq = $db->get_Seq_by_id('ROA1_HUMAN');
  16
  17   #
  18   # $seq is a Bio::Seq object
  19   #
  20
  21 =head1 DESCRIPTION
  22
  23 This is a pure interface class - in other words, all this does is define
  24 methods which other (concrete) classes will actually implement.
  25
  26 The Bio::DB::RandomAccessI class defines what methods a generic database class
  27 should have. At the moment it is just the ability to make Bio::Seq objects
  28 from a name (id) or an accession number.
  29
  30 =head1 CONTACT
  31
  32 Ewan Birney E<lt>birney@ebi.ac.ukE<gt> originally wrote this class.
  33
  34 =head2 Support
  35
  36 Please direct usage questions or support issues to the mailing list:
  37
  38 I<bioperl-l@bioperl.org>
  39
  40 rather than to the module maintainer directly. Many experienced and
  41 reponsive experts will be able look at the problem and quickly
  42 address it. Please include a thorough description of the problem
  43 with code and data examples if at all possible.
  44
  45 =head2 Reporting Bugs
  46
  47 Report bugs to the Bioperl bug tracking system to help us keep track
  48 the bugs and their resolution. Bug reports can be submitted via the web:
  49
  50   https://github.com/bioperl/bioperl-live/issues
  51
  52 =head1 APPENDIX
  53
  54 The rest of the documentation details each of the object
  55 methods. Internal methods are usually preceded with a _
  56
  57 =cut
  58
  59
  60 # Let the code begin...
  61
  62 package Bio::DB::RandomAccessI;
  63
  64 use strict;
  65
  66 use Bio::Root::RootI;
  67
  68 use base qw(Bio::Root::Root);
  69
  70 =head2 get_Seq_by_id
  71
  72  Title   : get_Seq_by_id
  73  Usage   : $seq = $db->get_Seq_by_id('ROA1_HUMAN')
  74  Function: Gets a Bio::Seq object by its name
  75  Returns : a Bio::Seq object or undef if not found
  76  Args    : the id (as a string) of a sequence,
  77
  78 =cut
  79
  80 sub get_Seq_by_id{
  81    my ($self,@args) = @_;
  82    $self->throw_not_implemented();
  83 }
  84
  85 =head2 get_Seq_by_acc
  86
  87  Title   : get_Seq_by_acc
  88  Usage   : $seq = $db->get_Seq_by_acc('X77802');
  89            $seq = $db->get_Seq_by_acc(Locus => 'X77802');
  90  Function: Gets a Bio::Seq object by accession number
  91  Returns : A Bio::Seq object or undef if not found
  92  Args    : accession number (as a string), or a two
  93                element list consisting of namespace=>accession
  94  Throws  : "more than one sequences correspond to this accession"
  95             if the accession maps to multiple primary ids and
  96             method is called in a scalar context
  97
  98 NOTE: The two-element form allows you to choose the namespace for the
  99 accession number.
 100
 101 =cut
 102
 103 sub get_Seq_by_acc{
 104    my ($self,@args) = @_;
 105    $self->throw_not_implemented();
 106 }
 107
 108
 109 =head2 get_Seq_by_version
 110
 111  Title   : get_Seq_by_version
 112  Usage   : $seq = $db->get_Seq_by_version('X77802.1');
 113  Function: Gets a Bio::Seq object by sequence version
 114  Returns : A Bio::Seq object
 115  Args    : accession.version (as a string)
 116  Throws  : "acc.version does not exist" exception
 117
 118 =cut
 119
 120
 121 sub get_Seq_by_version{
 122    my ($self,@args) = @_;
 123    $self->throw_not_implemented();
 124 }
 125
 126 ## End of Package
 127
 128 1;
 129