/usr/share/perl5/Bio/DB/Failover.pm is in libbio-perl-perl 1.7.2-2.
This file is owned by root:root, with mode 0o644.
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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 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 | # POD documentation - main docs before the code
=head1 NAME
Bio::DB::Failover - A Bio::DB::RandomAccessI compliant class which
wraps a prioritized list of DBs
=head1 SYNOPSIS
$failover = Bio::DB::Failover->new();
$failover->add_database($db);
# fail over Bio::DB::RandomAccessI.pm
# this will check each database in priority, returning when
# the first one succeeds
$seq = $failover->get_Seq_by_id($id);
=head1 DESCRIPTION
This module provides fail over access to a set of Bio::DB::RandomAccessI
objects.
=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://github.com/bioperl/bioperl-live/issues
=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::Failover;
use strict;
use base qw(Bio::Root::Root Bio::DB::RandomAccessI);
sub new {
my ($class,@args) = @_;
my $self = $class->SUPER::new(@args);
$self->{'_database'} = [];
return $self;
}
=head2 add_database
Title : add_database
Usage : add_database(%db)
Function: Adds a database to the Failover object
Returns : Count of number of databases
Args : Array of db resources
Throws : Not a RandomAccessI exception
=cut
sub add_database {
my ($self,@db) = @_;
for my $db ( @db ) {
if ( !ref $db || !$db->isa('Bio::DB::RandomAccessI') ) {
$self->throw("Database object $db is a not a Bio::DB::RandomAccessI");
next;
}
push(@{$self->{'_database'}},$db);
}
scalar @{$self->{'_database'}};
}
=head2 get_Seq_by_id
Title : get_Seq_by_id
Usage : $seq = $db->get_Seq_by_id('ROA1_HUMAN')
Function: Gets a Bio::Seq object by its name
Returns : a Bio::Seq object
Args : the id (as a string) of a sequence
Throws : "no id" exception
=cut
sub get_Seq_by_id {
my ($self,$id) = @_;
if( !defined $id ) {
$self->throw("no id is given!");
}
foreach my $db ( @{$self->{'_database'}} ) {
my $seq;
eval {
$seq = $db->get_Seq_by_id($id);
};
$self->warn($@) if $@;
if ( defined $seq ) {
return $seq;
} else {
$self->warn("No sequence retrieved by database " . ref($db));
}
}
return;
}
=head2 get_Seq_by_acc
Title : get_Seq_by_acc
Usage : $seq = $db->get_Seq_by_acc('X77802');
Function: Gets a Bio::Seq object by accession number
Returns : A Bio::Seq object
Args : accession number (as a string)
Throws : "no id" exception
=cut
sub get_Seq_by_acc {
my ($self,$id) = @_;
if( !defined $id ) {
$self->throw("no id is given!");
}
foreach my $db ( @{$self->{'_database'}} ) {
my $seq;
eval {
$seq = $db->get_Seq_by_acc($id);
};
$self->warn($@) if $@;
if ( defined $seq ) {
return $seq;
} else {
$self->warn("No sequence retrieved by database " . ref($db));
}
}
return;
}
=head2 get_Seq_by_version
Title : get_Seq_by_version
Usage : $seq = $db->get_Seq_by_acc('X77802.2');
Function: Gets a Bio::Seq object by versioned accession number
Returns : A Bio::Seq object
Args : accession number (as a string)
Throws : "acc does not exist" exception
=cut
sub get_Seq_by_version {
my ($self,$id) = @_;
if( !defined $id ) {
$self->throw("no acc is given!");
}
foreach my $db ( @{$self->{'_database'}} ) {
my $seq;
eval {
$seq = $db->get_Seq_by_version($id);
};
$self->warn($@) if $@;
if ( defined $seq ) {
return $seq;
} else {
$self->warn("No sequence retrieved by database " . ref($db));
}
}
return;
}
## End of Package
1;
__END__
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