Bio/DB/RandomAccessI.pm

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