/usr/share/perl5/Bio/DB/ReferenceI.pm is in libbio-perl-perl 1.6.924-3.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
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 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 | #
# BioPerl module for Bio::DB::ReferenceI
#
# Please direct questions and support issues to <bioperl-l@bioperl.org>
#
# Cared for by Chris Fields <cjfields at bioperl dot org>
#
# Copyright Chris Fields
#
# You may distribute this module under the same terms as perl itself
#
# POD documentation - main docs before the code
=head1 NAME
Bio::DB::ReferenceI - A RandomAccessI-like abstract interface for
retrieving Reference data from a sequence database and returning
Bio::Annotation::Reference objects
=head1 SYNOPSIS
#
# get a database object somehow using a concrete class
#
$ref = $db->get_Reference_by_id('123456');
#
# $ref is a Bio::Annotation::Reference 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::ReferenceI class defines methods used to retrieve reference data
from a sequence. This is returned in the form of Bio::Annotation::Reference
objects.
At the moment it is just the ability to make Bio::Annotation::Reference
objects from a name or unique id (id), an accession number (acc), and so on.
=head1 CONTACT
Ewan Birney originally wrote Bio::DB::RandomAccessI, from which this class
is based.
=head2 Mailing Lists
User feedback is an integral part of the
evolution of this and other Bioperl modules. Send
your comments and suggestions preferably to one
of the Bioperl mailing lists. Your participation
is much appreciated.
bioperl-l@lists.open-bio.org - General discussion
http://www.bioperl.org/wiki/Mailing_lists - About the mailing lists
=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://github.com/bioperl/bioperl-live/issues
=head1 AUTHOR
Email cjfields at bioperl dot org
=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::ReferenceI;
use strict;
=head2 get_Reference_by_id
Title : get_Reference_by_id
Usage : $ref = $db->get_Reference_by_id('123456')
Function: Gets a Bio::Annotation::Reference-implementing object by its name (id)
Returns : a Bio::Annotation::Reference object or undef if not found
Args : the id (as a string) of a sequence
=cut
sub get_Reference_by_id{
my ($self,@args) = @_;
$self->throw_not_implemented();
}
=head2 get_Reference_by_acc
Title : get_Reference_by_acc
Usage : $ref = $db->get_Reference_by_acc('X77802');
Function: Gets a Bio::Annotation::Reference object by accession number
Returns : A Bio::Annotation::Reference object or undef if not found
Args : accession number (as a string)
Throws : "more than one sequences correspond to this accession"
if the accession maps to multiple primary ids and
method is called in a scalar context
=cut
sub get_Reference_by_acc{
my ($self,@args) = @_;
$self->throw_not_implemented();
}
=head2 get_Reference_by_version
Title : get_Reference_by_version
Usage : $ref = $db->get_Reference_by_version('X77802.1');
Function: Gets a Bio::Annotation::Reference object by sequence version
Returns : A Bio::Annotation::Reference object
Args : accession.version (as a string)
Throws : "acc.version does not exist" exception
=cut
sub get_Reference_by_version{
my ($self,@args) = @_;
$self->throw_not_implemented();
}
## End of Package
1;
|