/usr/share/perl5/Bio/DB/RandomAccessI.pm is in libbio-perl-perl 1.6.923-1.
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1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 | # POD documentation - main docs before the code
#
#
=head1 NAME
Bio::DB::RandomAccessI - Abstract interface for a sequence database
=head1 SYNOPSIS
#
# get a database object somehow using a concrete class
#
$seq = $db->get_Seq_by_id('ROA1_HUMAN');
#
# $seq is a Bio::Seq object
#
=head1 DESCRIPTION
This is a pure interface class - in other words, all this does is define
methods which other (concrete) classes will actually implement.
The Bio::DB::RandomAccessI class defines what methods a generic database class
should have. At the moment it is just the ability to make Bio::Seq objects
from a name (id) or an accession number.
=head1 CONTACT
Ewan Birney E<lt>birney@ebi.ac.ukE<gt> originally wrote this class.
=head2 Support
Please direct usage questions or support issues to the mailing list:
I<bioperl-l@bioperl.org>
rather than to the module maintainer directly. Many experienced and
reponsive experts will be able look at the problem and quickly
address it. Please include a thorough description of the problem
with code and data examples if at all possible.
=head2 Reporting Bugs
Report bugs to the Bioperl bug tracking system to help us keep track
the bugs and their resolution. Bug reports can be submitted via the web:
https://redmine.open-bio.org/projects/bioperl/
=head1 APPENDIX
The rest of the documentation details each of the object
methods. Internal methods are usually preceded with a _
=cut
# Let the code begin...
package Bio::DB::RandomAccessI;
use strict;
use Bio::Root::RootI;
use base qw(Bio::Root::Root);
=head2 get_Seq_by_id
Title : get_Seq_by_id
Usage : $seq = $db->get_Seq_by_id('ROA1_HUMAN')
Function: Gets a Bio::Seq object by its name
Returns : a Bio::Seq object or undef if not found
Args : the id (as a string) of a sequence,
=cut
sub get_Seq_by_id{
my ($self,@args) = @_;
$self->throw_not_implemented();
}
=head2 get_Seq_by_acc
Title : get_Seq_by_acc
Usage : $seq = $db->get_Seq_by_acc('X77802');
$seq = $db->get_Seq_by_acc(Locus => 'X77802');
Function: Gets a Bio::Seq object by accession number
Returns : A Bio::Seq object or undef if not found
Args : accession number (as a string), or a two
element list consisting of namespace=>accession
Throws : "more than one sequences correspond to this accession"
if the accession maps to multiple primary ids and
method is called in a scalar context
NOTE: The two-element form allows you to choose the namespace for the
accession number.
=cut
sub get_Seq_by_acc{
my ($self,@args) = @_;
$self->throw_not_implemented();
}
=head2 get_Seq_by_version
Title : get_Seq_by_version
Usage : $seq = $db->get_Seq_by_version('X77802.1');
Function: Gets a Bio::Seq object by sequence version
Returns : A Bio::Seq object
Args : accession.version (as a string)
Throws : "acc.version does not exist" exception
=cut
sub get_Seq_by_version{
my ($self,@args) = @_;
$self->throw_not_implemented();
}
## End of Package
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