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1 # POD documentation - main docs before the code
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2 #
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3 # $Id: RandomAccessI.pm,v 1.12 2002/10/22 07:38:29 lapp Exp $
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4 #
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5
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6 =head1 NAME
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7
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8 Bio::DB::RandomAccessI - Abstract interface for a sequence database
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9
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10 =head1 SYNOPSIS
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11
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12 #
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13 # get a database object somehow using a concrete class
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14 #
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15
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16 $seq = $db->get_Seq_by_id('ROA1_HUMAN');
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17
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18 #
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19 # $seq is a Bio::Seq object
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20 #
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21
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22 =head1 DESCRIPTION
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23
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24 This is a pure interface class - in other words, all this does is define
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25 methods which other (concrete) classes will actually implement.
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26
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27 The Bio::DB::RandomAccessI class defines what methods a generic database class
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28 should have. At the moment it is just the ability to make Bio::Seq objects
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29 from a name (id) or a accession number.
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30
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31 =head1 CONTACT
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32
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33 Ewan Birney originally wrote this class.
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34
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35 =head2 Reporting Bugs
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36
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37 Report bugs to the Bioperl bug tracking system to help us keep track
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38 the bugs and their resolution. Bug reports can be submitted via email
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39 or the web:
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40
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41 bioperl-bugs@bio.perl.org
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42 http://bugzilla.bioperl.org/
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43
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44 =head1 APPENDIX
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45
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46 The rest of the documentation details each of the object
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47 methods. Internal methods are usually preceded with a _
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48
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49 =cut
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50
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51
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52 # Let the code begin...
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53
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54 package Bio::DB::RandomAccessI;
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55
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56 use vars qw(@ISA);
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57 use strict;
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58
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59 use Bio::Root::RootI;
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60 use Bio::Root::Root;
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61
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62 @ISA = qw(Bio::Root::Root);
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63
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64 =head2 get_Seq_by_id
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65
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66 Title : get_Seq_by_id
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67 Usage : $seq = $db->get_Seq_by_id('ROA1_HUMAN')
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68 Function: Gets a Bio::Seq object by its name
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69 Returns : a Bio::Seq object or undef if not found
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70 Args : the id (as a string) of a sequence,
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71
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72 =cut
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73
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74 sub get_Seq_by_id{
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75 my ($self,@args) = @_;
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76 $self->throw_not_implemented();
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77 }
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78
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79 =head2 get_Seq_by_acc
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80
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81 Title : get_Seq_by_acc
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82 Usage : $seq = $db->get_Seq_by_acc('X77802');
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83 $seq = $db->get_Seq_by_acc(Locus => 'X77802');
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84 Function: Gets a Bio::Seq object by accession number
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85 Returns : A Bio::Seq object or undef if not found
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86 Args : accession number (as a string), or a two
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87 element list consisting of namespace=>accession
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88 Throws : "more than one sequences correspond to this accession"
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89 if the accession maps to multiple primary ids and
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90 method is called in a scalar context
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91
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92 NOTE: The two-element form allows you to choose the namespace for the
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93 accession number.
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94
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95 =cut
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96
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97 sub get_Seq_by_acc{
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98 my ($self,@args) = @_;
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99 $self->throw_not_implemented();
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100 }
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101
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102
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103 =head2 get_Seq_by_version
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104
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105 Title : get_Seq_by_version
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106 Usage : $seq = $db->get_Seq_by_version('X77802.1');
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107 Function: Gets a Bio::Seq object by sequence version
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108 Returns : A Bio::Seq object
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109 Args : accession.version (as a string)
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110 Throws : "acc.version does not exist" exception
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111
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112 =cut
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113
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114
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115 sub get_Seq_by_version{
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116 my ($self,@args) = @_;
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117 $self->throw_not_implemented();
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118 }
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119
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120
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121
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122 ## End of Package
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123
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124 1;
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125
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