#
# BioPerl module for Bio::DB::SeqVersion
#
# Please direct questions and support issues to <bioperl-l@bioperl.org>
#
# Cared for by Brian Osborne
#
# Copyright Brian Osborne 2006
#
# You may distribute this module under the same terms as Perl itself
#
# POD documentation - main docs before the code
=head1 NAME
Bio::DB::SeqVersion - front end to querying databases for identifier
versions
=head1 SYNOPSIS
use Bio::DB::SeqVersion;
my $query = Bio::DB::SeqVersion->new(-type => 'gi');
my @all_gis = $query->get_all(2);
my $live_gi = $query->get_recent(2);
=head1 DESCRIPTION
The default type is 'gi'.
=head1 FEEDBACK
=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
the Bioperl mailing list. Your participation is much appreciated.
bioperl-l@bioperl.org - General discussion
http://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
of the bugs and their resolution. Bug reports can be submitted via
the web:
https://github.com/bioperl/bioperl-live/issues
=head1 AUTHOR - Brian Osborne
Email bosborne at alum.mit.edu
=head1 CONTRIBUTORS
Torsten Seemann - torsten.seemann AT infotech.monash.edu.au
=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::SeqVersion;
use strict;
use base qw(Bio::WebAgent Bio::Root::Root);
# Private class variable
my $DEFAULTIDTYPE = 'gi'; # sub default_id_type()
=head2 new()
Usage : my $obj = Bio::DB::SeqVersion->new();
Function: Create a Bio::DB::SeqVersion object
Returns : An instance of Bio::DB::SeqVersion
Args : -type Identifier namespace, default is 'gi'
=cut
sub new {
my($class,@args) = @_;
if( $class =~ /Bio::DB::SeqVersion::\S+/ ) {
my ($self) = $class->SUPER::new(@args);
$self->_initialize(@args);
return $self;
}
else {
my %param = @args;
@param{ map { lc $_ } keys %param } = values %param; # lowercase keys
# we delete '-type' so it doesn't get passed to the sub-class constructor
# note: delete() returns the value of the item deleted (undef if non-existent)
my $type = lc( delete($param{'-type'}) || $DEFAULTIDTYPE );
return unless( $class->_load_seqversion_module($type) );
# we pass %param here, not @args, as we have filtered out -type
return "Bio::DB::SeqVersion::$type"->new(%param);
}
}
=head2 get_recent()
Usage :
Function:
Example :
Returns :
Args :
=cut
sub get_recent {
my ($self,@args) = @_;
$self->throw_not_implemented();
}
=head2 get_all()
Usage :
Function:
Example :
Returns :
Args :
=cut
sub get_all {
my ($self,@args) = @_;
$self->throw_not_implemented();
}
=head2 _load_seqversion_module
Title : _load_seqversion_module
Usage : Used internally
Function: Loads up a module at run time on demand
Example :
Returns :
Args : Name of identifier type
=cut
sub _load_seqversion_module {
my ($self,$db) = @_;
my $module = "Bio::DB::SeqVersion::" . $db;
my $ok;
eval { $ok = $self->_load_module($module) };
if ( $@ ) {
print STDERR $@;
print STDERR <<END;
$self: $module cannot be found
Exception $@
For more information about the Bio::DB::SeqVersion system please see
the Bio::DB::SeqVersion docs.
END
;
}
return $ok;
}
=head2 default_id_type
Title : default_id_type
Usage : my $type = $self->default_id_type
Function: Returns default identifier type for this module
Returns : string
Args : none
=cut
sub default_id_type {
return $DEFAULTIDTYPE;
}
1;