———=head1 LICENSE
Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
Copyright [2016-2024] EMBL-European Bioinformatics Institute
Licensed under the Apache License, Version 2.0 (the "License");
you may not use this file except in compliance with the License.
You may obtain a copy of the License at
Unless required by applicable law or agreed to in writing, software
distributed under the License is distributed on an "AS IS" BASIS,
WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
See the License for the specific language governing permissions and
limitations under the License.
=cut
=head1 CONTACT
Please email comments or questions to the public Ensembl
developers list at <http://lists.ensembl.org/mailman/listinfo/dev>.
Questions may also be sent to the Ensembl help desk at
=head1 AUTHOR
Juguang Xiao <juguang@fugu-sg.org>
=cut
=head1 NAME
Bio::EnsEMBL::Utils::Converter::ens_bio
=head1 SYNOPISIS
You are not supposed to use this module directly. Please read
Bio::EnsEMBL::Utils::Converter
=head1 DESCRIPTION
This is a helper module to assist Bio::EnsEMBL::Utils::Converter find
which converter instance should be used, based on the -in and -out
parameters.
=head1 METHODS
=cut
$Bio::EnsEMBL::Utils::Converter::ens_bio::VERSION
=
'112.0.0_58'
;
# TRIAL
$Bio::EnsEMBL::Utils::Converter::ens_bio::VERSION
=
'112.0.058'
;
use
strict;
@ISA
=
qw(Bio::EnsEMBL::Utils::Converter)
;
=head2 new
Please see Bio::EnsEMBL::Utils::Converter::new
=cut
sub
new {
my
(
$caller
,
@args
) =
@_
;
my
$class
=
ref
(
$caller
) ||
$caller
;
if
(
$class
eq
'Bio::EnsEMBL::Utils::Converter::ens_bio'
){
my
%params
=
@args
;
@params
{
map
{
lc
$_
}
keys
%params
} =
values
%params
;
my
$module
=
$class
->_guess_module(
$params
{-in},
$params
{-out});
return
undef
unless
(
$class
->_load_module(
$module
));
return
"$module"
->new(
@args
);
}
else
{
my
$self
=
$class
->SUPER::new(
@args
);
# $self->_initialize(@args);
return
$self
;
}
}
# Unlike bio_ens, ens_bio does not need _initialize method for analysis and
# contig information.
#
sub
_guess_module {
my
(
$self
,
$in
,
$out
) =
@_
;
my
$tail
;
if
(
$in
eq
'Bio::EnsEMBL::SeqFeature'
){
$tail
=
'ens_bio_seqFeature'
;
}
elsif
(
$in
eq
'Bio::Ens::EMBL::FeaturePair'
){
$tail
=
'ens_bio_featurePair'
;
}
else
{
$self
->throw(
"[$in] to [$out], not supported"
);
}
return
"Bio::EnsEMBL::Utils::Converter::$tail"
;
}
1;