———=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
=cut
=head1 NAME
Bio::EnsEMBL::Utils::Tree::Interval::Mutable
=head1 SYNOPSIS
# start with an empty tree
my $tree = Bio::EnsEMBL::Utils::Tree::Interval::Mutable->new();
# add a few intervals (i.e. Bio::EnsEMBL::Utils::Interval)
$tree->insert($i1);
$tree->insert($i2);
$tree->insert($i3);
# query the tree
my $result = $tree->search(85, 100);
if (scalar @{$result}) {
print "Found overlapping interval: [", $result->[0]->start, ', ', $result->[0]->end, "\n";
}
=head1 DESCRIPTION
Class representing a dynamic, i.e. mutable, interval tree implemented as an augmented AVL balanced binary tree.
This module is a wrapper around two possible implementations: one using the Perl extension (XS) mechanisms, and
a pure Perl (PP) one.
The module is capable of detecting whether the XS module is available and it loads it in that
case; it falls back to the PP implementation otherwise.
=head1 METHODS
=cut
$Bio::EnsEMBL::Utils::Tree::Interval::Mutable::VERSION
=
'113.0.0'
;
use
strict;
# the modules providing the underlying implementation,
# either XS or pure perl fallback
my
$XS
=
'Bio::EnsEMBL::XS::Utils::Tree::Interval::Mutable'
;
my
$PP
=
'Bio::EnsEMBL::Utils::Tree::Interval::Mutable::PP'
;
# if XS is used, version at least 1.3.1 is required (provides the interval tree library)
my
$VERSION_XS
=
'1.3.1'
;
my
@public_methods
=
qw/ insert search remove size /
;
# import either XS or PP methods into namespace
unless
(
$Bio::EnsEMBL::Utils::Tree::Interval::Mutable::IMPL
) {
# first check if XS is available and try to load it,
# otherwise fall back to PP implementation
_load_xs() or _load_pp() or throw
"Couldn't load implementation: $@"
;
}
=head2 new
Arg [] : none
Example : my $tree = Bio::EnsEMBL::Utils::Tree::Mutable();
Description : Constructor. Creates a new mutable tree instance
Returntype : Bio::EnsEMBL::Utils::Tree::Interval::Mutable
Exceptions : none
Caller : general
=cut
sub
new {
my
$caller
=
shift
;
my
$class
=
ref
(
$caller
) ||
$caller
;
# for ($XS|$PP)::new(0);
return
eval
qq| $Bio::EnsEMBL::Utils::Tree::Interval::Mutable::IMPL\::new( \$caller ) |
unless
$caller
;
## no critic
if
(
my
$self
=
$Bio::EnsEMBL::Utils::Tree::Interval::Mutable::IMPL
->new(
@_
)) {
$self
->{_IMPL} =
$Bio::EnsEMBL::Utils::Tree::Interval::Mutable::IMPL
;
bless
(
$self
,
$class
);
return
$self
}
return
;
}
sub
_load_xs {
_load(
$XS
,
$VERSION_XS
);
}
sub
_load_pp {
_load(
$PP
);
}
sub
_load {
my
(
$module
,
$version
) =
@_
;
$version
||=
''
;
eval
qq| use $module $version |
;
## no critic
info(
sprintf
(
"Cannot load %s interval tree implementation"
,
$module
eq
$XS
?
'XS'
:
'PP'
), 2000)
and
return
if
$@;
push
@Bio::EnsEMBL::Utils::Tree::Interval::Mutable::ISA
,
$module
;
$Bio::EnsEMBL::Utils::Tree::Interval::Mutable::IMPL
=
$module
;
local
$^W;
no
strict
qw(refs)
;
## no critic
for
my
$method
(
@public_methods
) {
*{
"Bio::EnsEMBL::Utils::Tree::Interval::Mutable::$method"
} = \&{
"$module\::$method"
};
}
return
1;
}
1;